writeGSEAfiles: Write GSEA files

In scfurl/seqGlue: Makes sequencing data come together like glue

Write GSEA files

Description

GSEA formats are cumbersome. This function writes working .GCT and .CLS files for use in a variety of GSEA software including but not limited to the desktop (Java) application and the java cli.

Usage

writeGSEAfiles(
  object,
  class_labels,
  gene_labels = "gene_short_name",
  gct_filename = "data.gct",
  cls_filename = "data.cls",
  normalized = TRUE
)

Arguments

object	the object from which function will extract data. Currently supported objects include: 1) DESeq2 object and 2) Bioconductor expression set.
class_labels	the meta data column name (as a string) whose data will be written into the .CLS file.
gene_labels	the column name of the feature data that contains the desired name of .GCT rownames (ie genes; default is "gene_short_name").
gct_filename	filename of the .GCT file.
cls_filename	filename of the .CLS file.

References

Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 (2014)

Orchestrating high-throughput genomic analysis with Bioconductor. W. Huber, V.J. Carey, R. Gentleman, ..., M. Morgan Nature Methods, 2015:12, 115.

scfurl/seqGlue documentation built on Sept. 1, 2024, 11:20 a.m.