simpleDESeqReport: Simple DESeq report

In TapscottLab/SeqPipelineTools: Pipeline tools for RNA-seq or ChIP-seq data

Description

This function generates a simple CSV file of the DESeq analysis results and annotation.

Usage

simpleDESeqReport(dds, OrgDb, lfcThreshold = 0,
    gene_id_type = c("ENTREZID", "ENSEMBL"),
    thres.padj = NULL, filename)

Arguments

dds	A 'DESeqDataSet' object returned by DESeq.
OrgDb	An orgDb object in which the annotatio is obtained.
lfcThreshold	A numeric specifying the log fold change that the hypothesis tests are based upon.
gene_id_type	A character string that is either "ENTREZID" or "ENSEMBL".
thres.padj	Default to NULL. If NULL, returns statistical results and annotation for the whole set of genes. If given a fractional number, the results will be truncated accordingly.
filename	A character string specifying the destination and the filename of the return. The extension is preferred to be ".csv".

Value

A DataFrame instance containing the results of DESeq with annotation provided by the organic database, OrgDb.

Author(s)

Chao-Jen Wong

See Also

results

Examples

## Not run: 
library(org.Hs.eg.db)
pkgDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/canFam3.DuxFamily"
dds <- get(load(file.path(pkgDir, "data", "HinH.ens.dds.rda")))
filename <- file.path(pkgDir, "inst", "stats", "testing.csv")
df <- simpleDESeqReport(dds, OrgDb=org.Hs.eg.db, gene_id_type="ENTREZID",
    lfcThreshold=1, thres.padj=0.1, 
    filename=filename)

## End(Not run)

TapscottLab/SeqPipelineTools documentation built on May 16, 2019, 2:28 a.m.