plot_expression: plot_expression

In BoevaLab/CHIPIN: ChIP-seq Intersample Normalization

plot_expression

Description

Use plot_expression to profile the average ChIP-seq signal around gene TSS according to gene expression values.

Usage

plot_expression(TPM, RPKM=NULL, raw_read_count=NULL, path_to_bw, organism, output_dir = ".", histone_mark = "ChIP-seq signal")

Arguments

TPM	path to a gene expression file (TPM values): first column should contain gene names (official gene symbol), each following column should correspond to one sample/condition. The order of values should correspond to the order of .bigWig files in "path_to_bw". If you provide the "TPM" parameter, do not use the "raw_read_count" parameter or the "RPKM" parameter. Default: NULL.
RPKM	path to a gene expression file (RPKM values): first column should contain gene names (official gene symbol), each following column should correspond to one sample/condition. The order of values should correspond to the order of .bigWig files in "path_to_bw". If you provide the "RPKM" parameter, do not use the "raw_read_count" parameter or the "TPM" paramter. Default: NULL
raw_read_count	path to a gene expression file (raw read count values): first column should contain gene names (official gene symbol), each following column should correspond to one sample/condition. The order of values should correspond to the order of .bigWig files in "path_to_bw". Raw read count values will be transformed into RPKM values using information on exon lengths. If you provide the "raw_read_count" parameter, do not use the "RPKM" parameter or the "TPM" parameter. Default: NULL
path_to_bw	a vector containing paths to .bigWig files of the samples/conditions of interest. ! Mandatory parameter with no default value
output_dir	path to the output directory where one wants to store the ouput files. This directory should be created before running the function. Default: "."
organism	reference genome: "mm10", "mm9", "hg38" or "hg19". ! Mandatory parameter with no default value
histone_mark	name of the histone mark of interest; used to plot legends. Default: "ChIP-seq signal"

Author(s)

Lélia Polit, BoevaLab, "Computational Epigenetics of Cancer", Inserm, CNRS, Cochin Institute, Paris, France

Examples

#initialize parameters:
pathToRPKMfile = system.file("extdata", "FPKM_values_CLBBER_CLBMA_SJNB12.txt", package = "CHIPIN")
pathToFiles = system.file("extdata", c("CLBBER.K27ac.rep3.bw","SJNB12.K27ac.rep3.bw","CLBMA.K27ac.rep3.bw"), package = "CHIPIN")
outputFolder="." #change it if needed; create the corresponding output folder if it does not exists
histoneMarkName="H3K27Ac"

#run plotting function:
plot_expression(RPKM = pathToRPKMfile, path_to_bw = pathToFiles, organism="hg19", output_dir = outputFolder, histone_mark = histoneMarkName)

BoevaLab/CHIPIN documentation built on Feb. 1, 2024, 11:51 p.m.