seqc.diff.example: seqc.diff.example

In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Description

Compares differential expression analysis (DEA) methods using the diff.seqc function, and produces ROC-like plots.

Usage

seqc.diff.example(e = NULL, site = "BGI", tests = c("edgeR", "voom",
  "DESeq2"), between.groups = 1:5, inner.groups = list(c(1, 2, 3), c(4, 5)),
  do.plot = TRUE, returnData = FALSE)

Arguments

e	The count matrix or data.frame. Anything can be used as row names (e.g. gene symbols, transcript ids...). If NULL, the 'site' parameter is used to fetch the quantification from the seqc package (if installed).
site	If 'e' is NULL, data from the specified sequencing site will be fetched from the seqc package. Default BGI.
tests	A vector of the DEA methods to be compared.
between.groups	A vector of integers from 1 to 5 indicating the replicates to be used for comparison across conditions. Default 1:5.
inner.groups	A list of two vectors, each containing the replicates to be used for comparison inside each condition. Default list(c(1,2,3),c(4,5)).
do.plot	Logical, whether to produce Positives plots (see posplot). Default TRUE.
returnData	Logical, whether to return the resulting data.

Value

Produces a plot, and returns a list if returnData=TRUE.

plger/RNAontheBENCH documentation built on May 25, 2019, 8:22 a.m.