fad_RNAseq_diffAnalysis: Perform a Quick differential analysis of RNAseq data.

In magrichard/dmprocr: A R package that performs differential methylation profiles clustering

Perform a Quick differential analysis of RNAseq data.

Description

Perform a quick differential analysis of transcriptomic data (RNAseq) using non parametric test.

Usage

fad_RNAseq_diffAnalysis(data_trscr, exp_grp, gene_list,
  filter_indiv = "no_filter", contrast = c("tissue_status", "patho",
  "normal"), apply_func = apply)

Arguments

data_trscr	A data matrix that contains transcriptome information (RNAseq counts from HTseq). Columns correspond to indivuals, row correspond to genes.
exp_grp	A exp_grp dataframe that contains metadatas on data_trscr individuals.
gene_list	A gene_list bedfile containing the genes to screen for differential expression.
filter_indiv	A vector of individual names to be screened for differential expression. Optionnal (set on "no_filter" by default).
contrast	A vector containing the constrast to be used to estimate the logarithmic fols change. By default: c("tissue_status","patho","normal")
apply_func	Function to be used for apply.

Value

A gene_list table including log2FoldChange and adjusted p-value (padj) computed by DESeq2 and a data_ntrscr matrix of normalized counts.

magrichard/dmprocr documentation built on July 21, 2023, 11:01 p.m.