read_chip: Read CHIP file
In ribiosIO: Input/Output Utilities of the 'ribios' Suite

read_chip

R Documentation

Read CHIP file

Description

The CHIP file format is commonly used to annotate probesets or other identifiers to gene symbols and gene names. This function imports CHIP files, using a C procedure to accelerate the speed.

Usage

read_chip(x)

Arguments

x

File name

Details

The current implementation only parses the first three columns and ignores the rest of columns. This behavior may change in future versions to provide larger flexibility of parsing CHIP-like files.

Value

A data.frame is returned with three columns: ProbeSetID, GeneSymbol and GeneTitle. The column names are concordant with the GSEA convention, except that the empty spaces are omitted.

Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>

References

BROAD institute GSEA manual, available at https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats.

Examples


  testFile <- system.file("extdata/test.chip", package="ribiosIO")
  testChip <- read_chip(testFile)
  head(testChip)
  stopifnot(identical(colnames(testChip), c("ProbeSetID", "GeneSymbol", "GeneTitle")))

ribiosIO documentation built on Feb. 20, 2026, 5:09 p.m.