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03a_calculate_isomorphism_classes_fasta.R
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library(igraph) # for functionality regarding (bipartite graphs)
library(pbapply) # for progress bars for apply functions
source("helper_functions/calculate_biadjacency_matrix_and_submatrices.R")
source("helper_functions/duplicated_for_sparse_matrices.R")
source("helper_functions/isomorph_classes_calculation_and_plotting_functions.R")
################################################################################
#### calculate connected components (subgraphs) from biadjacency matrix ####
################################################################################
#### D1_fasta_min5AA (without isoforms)
matrix_01 <- readRDS("data/D1/D1_fasta/preprocessed/01_matrix_based_on_complete_fasta_D1_fasta.rds")
ind <- which(colSums(matrix_01) == 0) # proteins that do not have peptides anymore
matrix_01 <- matrix_01[,-ind]
saveRDS(matrix_01, "data/D1/D1_fasta/preprocessed/01_matrix_D1_fasta_min5AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min5AA.rds")
saveRDS(subgraphs, file = "data/D1/D1_fasta/preprocessed/Subgraphs_D1_fasta_min5AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min5AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min5AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min5AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min5AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min5AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D1/D1_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D1_fasta_min5AA_fast.RData")
################################################################################
#### D1_fasta_min6AA (without isoforms)
matrix_01 <- readRDS("data/D1/D1_fasta/preprocessed/01_matrix_based_on_complete_fasta_D1_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 6) # too small peptides
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0) # proteins that do not have peptides anymore
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D1/D1_fasta/preprocessed/01_matrix_D1_fasta_min6AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min6AA.rds")
saveRDS(subgraphs, file = "data/D1/D1_fasta/preprocessed/Subgraphs_D1_fasta_min6AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min6AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min6AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min6AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min6AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min6AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D1/D1_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D1_fasta_min6AA_fast.RData")
################################################################################
#### D1_fasta_min7AA (without isoforms)
matrix_01 <- readRDS("data/D1/D1_fasta/preprocessed/01_matrix_based_on_complete_fasta_D1_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 7)
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0) # proteins that do not have peptides anymore
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D1/D1_fasta/preprocessed/01_matrix_D1_fasta_min7AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min7AA.rds")
saveRDS(subgraphs, file = "data/D1/D1_fasta/preprocessed/Subgraphs_D1_fasta_min7AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min7AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = FALSE)
saveRDS(S_proteingroups, file = "data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min7AA.rds")
#### collapse peptide nodes
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min7AA.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min7AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min7AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D1/D1_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D1_fasta_min7AA_fast.RData")
################################################################################
#### D1_fasta_min9AA (without isoforms)
matrix_01 <- readRDS("data/D1/D1_fasta/preprocessed/01_matrix_based_on_complete_fasta_D1_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 9)
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0) # proteins that do not have peptides anymore
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D1/D1_fasta/preprocessed/01_matrix_D1_fasta_min9AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min9AA.rds")
saveRDS(subgraphs, file = "data/D1/D1_fasta/preprocessed/Subgraphs_D1_fasta_min9AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_D1_fasta_min9AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = FALSE)
saveRDS(S_proteingroups, file = "data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min9AA.rds")
#### collapse peptide nodes
S <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_proteingroups_D1_fasta_min9AA.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min9AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D1/D1_fasta/preprocessed/Submatrix_merged_Peptides_D1_fasta_min9AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D1/D1_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D1_fasta_min9AA_fast.RData")
################################################################################
################################################################################
################################################################################
#### D2_fasta_min5AA (without isoforms)
matrix_01 <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_based_on_complete_fasta_D2_fasta.rds")
ind <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind]
saveRDS(matrix_01, "data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_D2_fasta_min5AA.rds")
matrix_01 <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_D2_fasta_min5AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min5AA.rds")
saveRDS(subgraphs, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Subgraphs_D2_fasta_min5AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min5AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min5AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min5AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min5AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min5AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D2_without_isoforms/D2_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D2_fasta_min5AA_fast.RData")
################################################################################
#### D2_fasta_min6AA (without isoforms)
matrix_01 <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_based_on_complete_fasta_D2_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 6)
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_D2_fasta_min6AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min6AA.rds")
saveRDS(subgraphs, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Subgraphs_D2_fasta_min6AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min6AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = FALSE)
saveRDS(S_proteingroups, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min6AA.rds")
#### collapse peptide nodes
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min6AA.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min6AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min6AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D2_without_isoforms/D2_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D2_fasta_min6AA_fast.RData")
################################################################################
#### D2_fasta_min7AA (without isoforms)
matrix_01 <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_based_on_complete_fasta_D2_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 7)
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_D2_fasta_min7AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min7AA.rds")
saveRDS(subgraphs, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Subgraphs_D2_fasta_min7AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min7AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min7AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min7AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min7AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min7AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D2_without_isoforms/D2_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D2_fasta_min7AA_fast.RData")
################################################################################
#### D2_fasta_min9AA (without isoforms)
matrix_01 <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_based_on_complete_fasta_D2_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 9)
matrix_01 <- matrix_01[-ind,]
ind2 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind2]
saveRDS(matrix_01, "data/D2_without_isoforms/D2_fasta/preprocessed/01_matrix_D2_fasta_min9AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min9AA.rds")
saveRDS(subgraphs, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Subgraphs_D2_fasta_min9AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_D2_fasta_min9AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min9AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_proteingroups_D2_fasta_min9AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min9AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D2_without_isoforms/D2_fasta/preprocessed/Submatrix_merged_Peptides_D2_fasta_min9AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D2_without_isoforms/D2_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D2_fasta_min9AA_fast.RData")
################################################################################
################################################################################
################################################################################
#### D3_fasta_min5AA (without isoforms)
matrix_01 <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta_without_isoform.rds")
ind <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind]
saveRDS(matrix_01, "data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_D3_without_isoforms_fasta_min5AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min5AA.rds")
saveRDS(subgraphs, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Subgraphs_D3_without_isoforms_fasta_min5AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min5AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min5AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min5AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min5AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min5AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3_without_isoforms/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_without_isoforms_fasta_min5AA_fast.RData")
################################################################################
#### D3_fasta_min6AA (without isoforms)
matrix_01 <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta_without_isoform.rds")
ind <- which(nchar(rownames(matrix_01)) < 6)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_D3_without_isoforms_fasta_min6AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min6AA.rds")
saveRDS(subgraphs, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Subgraphs_D3_without_isoforms_fasta_min6AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min6AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min6AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min6AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min6AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min6AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3_without_isoforms/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_without_isoforms_fasta_min6AA_fast.RData")
################################################################################
#### D3_fasta_min7AA (without isoforms)
matrix_01 <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta_without_isoform.rds")
ind <- which(nchar(rownames(matrix_01)) < 7)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_D3_without_isoforms_fasta_min7AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min7AA.rds")
saveRDS(subgraphs, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Subgraphs_D3_without_isoforms_fasta_min7AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min7AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min7AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min7AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min7AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min7AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3_without_isoforms/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_without_isoforms_fasta_min7AA_fast.RData")
#################################################################################
#### D3_fasta_min9AA (without isoforms)
matrix_01 <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta_without_isoform.rds")
ind <- which(nchar(rownames(matrix_01)) < 9)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3_without_isoforms/D3_fasta/preprocessed/01_matrix_D3_without_isoforms_fasta_min9AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min9AA.rds")
saveRDS(subgraphs, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Subgraphs_D3_without_isoforms_fasta_min9AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_D3_without_isoforms_fasta_min9AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min9AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_proteingroups_D3_without_isoforms_fasta_min9AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min9AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3_without_isoforms/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_without_isoforms_fasta_min9AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3_without_isoforms/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_without_isoforms_fasta_min9AA_fast.RData")
################################################################################
################################################################################
################################################################################
#### D3_fasta_min5AA (with isoforms)
matrix_01 <- readRDS("data/D3/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta.rds")
ind <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-ind]
saveRDS(matrix_01, "data/D3/D3_fasta/preprocessed/01_matrix_D3_fasta_min5AA.rds")
matrix_01 <- readRDS("data/D3/D3_fasta/preprocessed/01_matrix_D3_fasta_min5AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min5AA.rds")
saveRDS(subgraphs, file = "data/D3/D3_fasta/preprocessed/Subgraphs_D3_fasta_min5AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min5AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min5AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min5AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min5AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min5AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_fasta_min5AA_fast.RData")
################################################################################
#### D3_fasta_min6AA (with isoforms)
matrix_01 <- readRDS("data/D3/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 6)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3/D3_fasta/preprocessed/01_matrix_D3_fasta_min6AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min6AA.rds")
saveRDS(subgraphs, file = "data/D3/D3_fasta/preprocessed/Subgraphs_D3_fasta_min6AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min6AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min6AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min6AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min6AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min6AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_fasta_min6AA_fast.RData")
################################################################################
#### D3_fasta_min7AA (with isoforms)
matrix_01 <- readRDS("data/D3/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 7)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3/D3_fasta/preprocessed/01_matrix_D3_fasta_min7AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min7AA.rds")
saveRDS(subgraphs, file = "data/D3/D3_fasta/preprocessed/Subgraphs_D3_fasta_min7AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min7AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min7AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min7AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min7AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min7AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_fasta_min7AA_fast.RData")
################################################################################
#### D3_fasta_min9AA (with isoforms)
matrix_01 <- readRDS("data/D3/D3_fasta/preprocessed/01_matrix_based_on_complete_fasta_D3_fasta.rds")
ind <- which(nchar(rownames(matrix_01)) < 9)
matrix_01 <- matrix_01[-ind,]
inD3 <- which(colSums(matrix_01) == 0)
matrix_01 <- matrix_01[,-inD3]
saveRDS(matrix_01, "data/D3/D3_fasta/preprocessed/01_matrix_D3_fasta_min9AA.rds")
G <- igraph::graph_from_incidence_matrix(matrix_01) # calculate complete bipartite graph
subgraphs <- igraph::decompose(G) # calculate connected components
### back to sub-adjacency matrices
Submatrix <- pblapply(subgraphs, as_incidence_matrix, sparse = TRUE)
Submatrix <- pblapply(Submatrix, as, "dgCMatrix")
saveRDS(Submatrix, file = "data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min9AA.rds")
saveRDS(subgraphs, file = "data/D3/D3_fasta/preprocessed/Subgraphs_D3_fasta_min9AA.rds")
#### collapse protein nodes:
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_D3_fasta_min9AA.rds")
S_proteingroups <- form_proteingroups(S, sparse = TRUE, fast = TRUE)
saveRDS(S_proteingroups, file = "data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min9AA_fast.rds")
#### collapse peptide nodes
S <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_proteingroups_D3_fasta_min9AA_fast.rds")
Submatrix_merged_Peptides <- merge_Peptides(S, sparse = TRUE, fc = FALSE, fast = TRUE)
saveRDS(Submatrix_merged_Peptides, file = "data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min9AA_fast.rds")
#### calculate isomorphism classes
Submatrix_merged_Peptides <- readRDS("data/D3/D3_fasta/preprocessed/Submatrix_merged_Peptides_D3_fasta_min9AA_fast.rds")
isomorph <- calculateIsomorphList(Submatrix_merged_Peptides)
save(isomorph, file = "data/D3/D3_fasta/isomorph_classes/isomorph_classes_merged_Peptides_D3_fasta_min9AA_fast.RData")