define_batches: Define batches based on scan date

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

Define batches based on scan date

Description

Groups samples into batches based on scan date. Samples run within a short time interval can be defined to belong to the same batch.

Usage

define_batches(se, col.scan.date = "scan.date", diff.ignore = 1)

Arguments

se	[SummarizedExperiment-class object] study data set
col.scan.date	[character(1)] Column in colData() with scan dates (default: scan.date as generated by the function extract_scan_date
diff.ignore	[numeric(1)] Time difference (in days) defined as negligible (default: 1)

Value

SummarizedExperiment-class object with batch information added as column batch in colData()

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