s3_DE_analysis: s3 differential gene analysis

In galelab/GaleGEAnalysis: What the Package Does (One Line, Title Case)

Description

This function runs differential gene analysis (linear modeling on normalized counts)

Usage

s3_DE_analysis(
  targetfile = "./p1_modified_count_matrix_results/target_file.csv",
  folder2voomobjects = "s1_norm_raw_counts_results",
  results_folder = FALSE,
  gene_conversion_file = FALSE,
  blocking_column = FALSE,
  matrixfile = FALSE,
  pvalue = 0.05,
  logfoldchange = 1.5,
  reset_design_matrix = FALSE,
  target_columns = FALSE,
  batch_column = FALSE
)

Arguments

targetfile	target file.
folder2voomobjects	folder where necessary voom R objects are stored (should be results folder from step 1) defualt is s1_norm_raw_counts_results
results_folder	User can specify name of output folder they want results to go in (default is s3_DE_results/)
gene_conversion_file	file with alternative gene names (we usually convert Rhesus Ensembl genes to HGNC)
blocking_column	column to account sampling from the same animal multiple times (needs to be the same as whatever was specified in step s1_normalize_raw_counts)
matrixfile	text file outlining different contrasts to do in DE analysis
pvalue	parameter for determining significantly DE genes (default 0.05)
logfoldchange	parameter for determining significantly DE genes (default 1.5)
reset_design_matrix	parameter for user to reset design matrix if they want to do this differently than they did in step 1 (defualt is FALSE)
target_columns	vector of columns from target file to use as treatment group, this needs to be set if reset_design_matrix is TRUE
batch_column	column from target file to be used as batch effect if reseting design matrix

Examples

s3_DE_analysis(countfile="./s1_norm_raw_counts_results/1.norm_matrix.txt", targetfile="./p1_modified_count_matrix_results/target_file.csv", gene_conversion_file="rhesus2human.csv", blocking_column=2, matrixfile="./MATRIX.txt")

galelab/GaleGEAnalysis documentation built on May 18, 2020, 7:32 a.m.