View source: R/trscr_analysis.R
RNAseq_diffAnalysis | R Documentation |
Perform differential analysis of transcriptomic data (RNAseq) using DESeq2 R package.
RNAseq_diffAnalysis(data_trscr, exp_grp, gene_list,
filter_indiv = "no_filter", alpha = 0.05, contrast = c("tissue_status",
"patho", "normal"), fitType = "parametric",
normalization_factor = "no_factor")
data_trscr |
A |
exp_grp |
A |
gene_list |
A |
filter_indiv |
A vector of individual names to be screened for differential expression. Optionnal (set on "no_filter" by default). |
alpha |
A parameter to indicate the significance cutoff used by |
contrast |
A vector containing the constrast to be used to estimate the logarithmic fols change. By default: c("tissue_status","patho","normal") |
fitType |
A DESeq fitting paramater, by default set to "parametric" |
normalization_factor |
A matrix of normalization to preempt DESeq2 sizeFactors. Optionnal (set on "no_factor" by default). |
A gene_list
table including log2FoldChange and adjusted p-value (padj) computed by DESeq2 and a data_ntrscr
matrix of normalized counts.
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