package contents

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: microsig
+Type: Package
+Title: Calculates Microbe Signature Score
+Version: 0.0.0.9000
+Authors@R: 
+    c(person(given = "Caroline",
+           family = "Wheeler",
+           role = c("aut"),
+           comment = c(ORCID = "0000-0002-3374-4909")),
+      person(given = "Rebecca", 
+            family = "Hoyd",
+            role = c("aut"),
+           comment = c(ORCID = "0000-0003-1210-4491")),
+      person(given = "Daniel",
+           family = "Spakowicz",
+           role = c("aut", "cre"),
+           email = "daniel.spakowicz@osumc.edu",
+           comment = c(ORCID = "0000-0003-2314-6435"))
+Maintainer: Daniel Spakowicz <daniel.spakowicz@osumc.edu>
+Description: This package contains functions to calculate microbe signatures, particularly from bugsigdb inputs. 
+License: MIT
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: 
+    dplyr,
+    tidyr

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(calcMicroSigScore)
+export(getSigList)
+export(microbeEntries)
+import(dplyr)
+import(tidyr)

R/calcMicroSigScore.R

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+#' Function to calculate microbe signature scores given a set of up and down
+#' regulated microbes and the relative abundances of microbe per sample
+#'
+#' @param taxa a data frame where columns are microbes and rows are samples, first
+#'    column named 'sample'
+#' @param sig.up a character vector listing microbes in given signature that are
+#'    up-regulated, empty if none
+#' @param sig.down a character vector listing microbes in given signature that are
+#'    down-regulated, empty if none
+#'
+#' @return a data frame with samples and corresponding microbe signature scores
+#'
+#' @import dplyr
+#' @import tidyr
+#'
+#' @export
+calcMicroSigScore <- function(taxa, sig.up, sig.down){
+  df <- taxa %>%
+    tidyr::gather(microbe, exo.ra, -sample) %>%
+    dplyr::group_by(sample) %>%
+    dplyr::mutate(z_score = scale(exo.ra))
+
+  upMics <- df %>%
+    dplyr::filter(microbe %in% sig.up)
+
+  upTotal <- length(unique(upMics$microbe))
+
+  upMics <- upMics %>%
+    dplyr::group_by(sample) %>%
+    dplyr::summarize(tempUp = sum(exo.ra))
+
+  downMics <- df %>%
+    dplyr::filter(microbe %in% sig.down)
+
+  downTotal <- length(unique(downMics$microbe))
+
+  downMics <- downMics %>%
+    dplyr::group_by(sample) %>%
+    dplyr::summarize(tempDown = sum(exo.ra))
+
+  if(upTotal == 0 && downTotal == 0){
+    df <- data.frame(matrix(ncol = 0, nrow = 0))
+  }else if(upTotal == 0){
+    df <- downMics %>%
+      dplyr::mutate(score = tempDown*(1/downTotal)) %>%
+      dplyr::select(sample,score)
+  }else if(downTotal == 0){
+    df <- upMics %>%
+      dplyr::mutate(score = tempUp*(1/upTotal)) %>%
+      dplyr::select(sample, score)
+  }else{
+    df <- merge(upMics, downMics, by = "sample") %>%
+      dplyr::mutate(score = (tempUp - tempDown)*(1/(upTotal + downTotal))) %>%
+      dplyr::select(sample, score)
+  }
+
+  return(df)
+}

R/getSigList.R

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+#' Given a single cell value from bigsigDB output in the column 'MetaPhlAn.taxon.names',
+#' returns a list of the microbes
+#'
+#' @param sig character string from bugsigDB output containing comma separated
+#' Metaphlan taxonomic names
+#'
+#' @return sig.list , a character list of containing the string after the last
+#'  "|" in each comma separated Metaphlan taxonomic name
+#'
+#' @export
+getSigList <- function(sig){
+  sig.list <- sub("^.+\\|", "", unlist(strsplit(sig ,",")))
+  return(sig.list)
+}

R/microbeEntries.R

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+#' Microbe Entries
+#' A function that can be used to call of specific microbe signatures.
+#' @param query Name of the signature group. If query is passed "all" function will return all the signature groups
+#'
+#' @return The microbes within a desired signature group in the format "x__microbe name" with x indicating taxonomic level
+#' @export
+#'
+#' @examples microbeEntries("paa_up")
+microbeEntries <- function(query){
+
+  paa_up <- c("s__Clostridium sp. UNK-MGS-6", "s__Firmicutes bacterium CAG 41",
+              "s__Coprobacillus cateniformis", "s__Clostridia bacterium UC5-1-2G4",
+              "s__Streptococcus dysgalactiae", "s__Acidaminococcus sp. HPA0509",
+              "s__Roseburia sp.CAG-303", "s__Butyrivibrio_sp. AE2032",
+              "s__Coprobacillus sp. 29-1", "s__Coprobacillus sp. D6")
+  paa_down <- c("s__Alistipes sp. CAG-435", "s__Fusobacterium hwasookii",
+                "s__Leuconostoc sp. DORA-2", "s__Paenibacillus lentimorbus",
+                "s__Fusobacterium sp. oral taxon 370", "s__Alcanivorax hongdengensis",
+                "s__Arthrobacter sp. LS16", "s__Bacillus sp. 5B6", "s__Bacillus velezensis",
+                "s__Fusobacterium sp. OBRC1")
+
+  mic_list <- list(paa_up, paa_down)
+
+  names(mic_list) <- c("paa_up", "paa_down")
+
+  if(query == "all"){
+    return(mic_list)
+  }
+
+  mics_queried <- mic_list[[query]]
+  return(mics_queried)
+}

README.md

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 # microsig
-This package contains functions to calculate microbe signatures, particularly from bugsigdb inputs.
+This package contains functions to calculate microbe signature scores, particularly from bugsigdb inputs.

microsig.Rproj

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