extract_scan_date: Extract scan date

In szymczak-lab/harmonizeGeneExprData: Harmonization of gene expression data from GEO and ArrayExpress

Extract scan date

Description

Extracts date of scanning from original array files (e.g. CEL for Affymetrix and idat for Illumina arrays).

Usage

extract_scan_date(
  se,
  col.sample.id = "geo_accession",
  array.type = "affy",
  temp.dir = tempdir(),
  tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%m/%d/%Y", "%m/%d/%y",
    "%m-%d-%Y", "%d-%b-%Y")
)

Arguments

se	[SummarizedExperiment-class object] study data set
col.sample.id	[character(1)] Column in colData() with sample accession information (default: "geo_accession")
array.type	[character(1)] type of array ("affy" (default), "agilent" or "illumina")
temp.dir	[character(1)] directory where temporary files should be stored
tryFormats	[character(n)] Possible format strings to try when converting date as character to an object of class Date

Details

Currently only implemented for Affymetrix arrays.

Value

SummarizedExperiment-class object with scan date added as column scan.date in colData.

szymczak-lab/harmonizeGeneExprData documentation built on Dec. 1, 2022, 9:07 p.m.