edger_dge: Using 'edger_dge' for 'raw' counts

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

edger_dge uses the edgeR package to perform DGE analysis on raw_counts object.

Usage

edger_dge(x, ...)

## Default S3 method:
edger_dge(x, ...)

## S3 method for class 'raw_counts'
edger_dge(x, design, contrast, ...)

Arguments

x	An object of class raw_counts.
...	Additional arguments.
design	A design matrix. See construct_design.
contrast	Contrast to compute DGE for. See construct_contrasts.

Value

An object of class dge consisting of top tables from running the corresponding edger_dge method.

Note

The term differential gene expression or DGE is not used in a restrictive manner and applies to genomic features in general, i.e., genes, transcripts, exons etc.

See Also

rnaseq, gather_counts show_counts limma_dge construct_design construct_contrasts write_dge as.dgelist as.eset volcano_plot density_plot

Examples

path = system.file("tests", package="ganalyse")

# ----- raw ----- # 
raw_path = file.path(path, "raw", "annotation.txt")
raw_obj = rnaseq(raw_path, format="raw", experiment="sample")
raw_counts = gather_counts(raw_obj, by="gene-id", threshold=1L)
raw_design = construct_design(raw_counts, ~ 0 + condition)
raw_contrasts = construct_contrasts(
                     design = raw_design, 
                     treatA.vs.control = conditiontreatA-conditioncontrol, 
                     treatB.vs.control = conditiontreatB-conditioncontrol
                 )
# DE genes between treatA and control
edger_dge(raw_counts, design=raw_design, 
             contrast=raw_contrasts[, "treatA.vs.control"])
# DE genes between treatB and control
edger_dge(raw_counts, design=raw_design, 
             contrast=raw_contrasts[, "treatB.vs.control"])
# DE genes between any of the treatments
edger_dge(raw_counts, design=raw_design, contrast=raw_contrasts)

openanalytics/ganalyse documentation built on May 24, 2019, 2:25 p.m.