degResults: Complete report from DESeq2 analysis

degResultsR Documentation

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.