degResults: Complete report from DESeq2 analysis

In lpantano/DEGreport: Report of DEG analysis

Complete report from DESeq2 analysis

Description

Complete report from DESeq2 analysis

Usage

degResults(
  res = NULL,
  dds,
  rlogMat = NULL,
  name,
  org = NULL,
  FDR = 0.05,
  do_go = FALSE,
  FC = 0.1,
  group = "condition",
  xs = "time",
  path_results = ".",
  contrast = NULL
)

Arguments

res	output from DESeq2::results() function.
dds	DESeq2::DESeqDataSet() object.
rlogMat	matrix from DESeq2::rlog() function.
name	string to identify results
org	an organism annotation object, like org.Mm.eg.db. NULL if you want to skip this step.
FDR	int cutoff for false discovery rate.
do_go	boolean if GO enrichment is done.
FC	int cutoff for log2 fold change.
group	string column name in colData(dds) that separates samples in meaninful groups.
xs	string column name in colData(dss) that will be used as X axes in plots (i.e time)
path_results	character path where files are stored. NULL if you don't want to save any file.
contrast	list with character vector indicating the fold change values from different comparisons to add to the output table.

Value

ggplot2 object

Examples

data(humanGender)
library(DESeq2)
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], design=~group)
dse <- DESeq(dse)
res <- degResults(dds = dse, name = "test", org = NULL,
  do_go = FALSE, group = "group", xs = "group", path_results = NULL)

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.