noCNV_diffAnalysis: Calculate differential expression on a subset of patient.

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

Calculate differential expression on a subset of patient.

Description

Calculate differential expression on a subset of patient, in particular those with no CNV

Usage

noCNV_diffAnalysis(data_ntrscr, data_cnv, exp_grp, gene_list,
  filter_indiv = "no_filter", contrast = c("tissue_status", "patho",
  "normal"), no_cnv_filter = c(-0.2, 0.2))

Arguments

data_ntrscr	A data matrix that contains normalized RNAseq counts (from DESeq2 analysis). Columns correspond to indivuals, row correspond to genes.
data_cnv	A data matrix that contains CNV data
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")
no_cnv_filter	A vector of two values indicating the CNV values threshold for no CNV, by default set to c(-0.2, 0.2).

Value

A gene_list table including a noCNVlog2FC value associated with differential expression between sample without CNV.

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