From b28f04f93e795b134834fde8c8935a9b175206cb Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 20:54:54 +0200 Subject: [PATCH 1/7] information about exp_design --- README.md | 38 ++++++++++++++++++++++++++++++++++---- 1 file changed, 34 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d684137..561ec2a 100644 --- a/README.md +++ b/README.md @@ -17,12 +17,42 @@ You can install the development version of MEAanalysis from [GitHub](https://git devtools::install_github("ankemt/MEAanalysis") ``` -## Example +## Getting started -This is a basic example which shows you how to solve a common problem: +The MEAanalysis package is under active development. +### Create an inputfile with the experimental design + +This can be done with the following function: + +``` r +MEAanalysis::exp_design() +``` + +This call prompts a few questions: first, the date of the experiment and the experiment ID. +For example, the experiment `TestExperiment` done on October 3rd 2020: ``` r -library(MEAanalysis) -## basic example code +What is the date of the experiment? (YYYYMMDD) 20201003 +What is the experiment ID? TestExperiment +``` + +Then, you can add well ranges for the different experimental conditions. +For example, here is how to add a range of wells for the control: +``` r +What is the experimental condition? control +In what direction ('LR' for left-to-right or 'TB' for top-to-bottom) is the sequence of wells? TB +What is the first well in this category? (e.g.: A1) A1 +What is the last well in this category? (e.g.: F8) B2 +Do you want to add another group? (y/n) n +``` + +This generates the file `design.txt` saved in the current working directory, with the following content: +``` +Date: 20201003 +ExperimentID: TestExperiment +Total_wells: 48 +Groups: +control: A1 B1 C1 D1 E1 F1 A2 B2 ``` +This file can of course also be generated and edited by hand. From 6fe6be787eb592ba7aae52e91dc6170b3e5b56a3 Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:05:57 +0200 Subject: [PATCH 2/7] Add treatment_ratio info --- README.md | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 561ec2a..44e7109 100644 --- a/README.md +++ b/README.md @@ -19,9 +19,9 @@ devtools::install_github("ankemt/MEAanalysis") ## Getting started -The MEAanalysis package is under active development. +The MEAanalysis package is under active development. Currently, it can be used to create a tidy data object that aggregates data from baseline and exposure neural metrics files that are output files of the MEA device. -### Create an inputfile with the experimental design +### Step 1: create an inputfile with the experimental design This can be done with the following function: @@ -56,3 +56,19 @@ control: A1 B1 C1 D1 E1 F1 A2 B2 ``` This file can of course also be generated and edited by hand. +### Step 2: Calculate the experiment's treatment ratio + +For this function, three input files are required: +- The neural metrics for the baseline (a `.csv` file) +- The neural metrics for the exposure (a `.csv` file) +- The design file created under step 1. + +Calculate the treatment ratio as follows: +``` r +data <- MEAanalysis::treatment_ratio( + exposurepath = "path/to/exposurefile.csv", + baselinepath = "path/to/baselinefile.csv", + designpath = "path/to/design.txt") +``` + +The object created here contains the raw values from both input files (`Baseline_value` and `Exposure_value`) for all wells (included in the `design.txt` file) and parameters, as well as the `Treatment_ratio`, a calculation of exposure/baseline. From 17532e18ccf9499b275c980110246298fee6bcdb Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:17:04 +0200 Subject: [PATCH 3/7] add feedback info --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 44e7109..73848b7 100644 --- a/README.md +++ b/README.md @@ -72,3 +72,6 @@ data <- MEAanalysis::treatment_ratio( ``` The object created here contains the raw values from both input files (`Baseline_value` and `Exposure_value`) for all wells (included in the `design.txt` file) and parameters, as well as the `Treatment_ratio`, a calculation of exposure/baseline. + +## Trial use & feedback +We are very happy with your feedback! Please let us know your experience with this package by creating an [issue](https://github.com/ankemt/MEAanalysis/issues), or by emailing Anke Tukker directly at [atukker@purdue.edu](mailto:atukker@purdue.edu). From 28d542e0162fc6da4c770f5ccb725da7f2054b71 Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:17:45 +0200 Subject: [PATCH 4/7] Update README.md Co-authored-by: ankemt <44837671+ankemt@users.noreply.github.com> --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 73848b7..61a7c8b 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,6 @@ MEAanalysis::exp_design() This call prompts a few questions: first, the date of the experiment and the experiment ID. For example, the experiment `TestExperiment` done on October 3rd 2020: -``` r What is the date of the experiment? (YYYYMMDD) 20201003 What is the experiment ID? TestExperiment ``` From cfb085df93b666df0915663c0559e38ef485b30f Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:17:52 +0200 Subject: [PATCH 5/7] Update README.md Co-authored-by: ankemt <44837671+ankemt@users.noreply.github.com> --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 61a7c8b..af838e5 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,6 @@ What is the experiment ID? TestExperiment Then, you can add well ranges for the different experimental conditions. For example, here is how to add a range of wells for the control: -``` r What is the experimental condition? control In what direction ('LR' for left-to-right or 'TB' for top-to-bottom) is the sequence of wells? TB What is the first well in this category? (e.g.: A1) A1 From 4352d3fc733dce04fdbe892de2e6547f7d787843 Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:17:59 +0200 Subject: [PATCH 6/7] Update README.md Co-authored-by: ankemt <44837671+ankemt@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index af838e5..bdc3e9e 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,7 @@ Total_wells: 48 Groups: control: A1 B1 C1 D1 E1 F1 A2 B2 ``` -This file can of course also be generated and edited by hand. +This file can of course also be generated and edited by hand. At the moment the well range functionality only works for 48 well plates. If your input uses a different plate format the design file should be edited by hand. ### Step 2: Calculate the experiment's treatment ratio From d60574e9560979e4063dae2cb06af27d2ef26072 Mon Sep 17 00:00:00 2001 From: Barbara Vreede Date: Thu, 20 Apr 2023 21:18:06 +0200 Subject: [PATCH 7/7] Update README.md Co-authored-by: ankemt <44837671+ankemt@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bdc3e9e..e862656 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ devtools::install_github("ankemt/MEAanalysis") ## Getting started -The MEAanalysis package is under active development. Currently, it can be used to create a tidy data object that aggregates data from baseline and exposure neural metrics files that are output files of the MEA device. +This package is under active development. Currently, it can be used to create a tidy data object that aggregates data from baseline and exposure neural metrics output files. ### Step 1: create an inputfile with the experimental design