extract_scan_date: Extract scan date

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

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",
  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	RangedSummarizedExperiment-class object
col.sample.id	Character or integer vector. Column in colData() with sample information.
temp.dir	Character. Destination directory to downloaded array files.
tryFormats	Character vector. Format strings for date to try.

Value

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

Examples

data("se.probeset")

se.probeset = extract_scan_date(se = se.probeset)

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.