dot-makeLabels: Perform the checks and return the labels

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

Perform the checks and return the labels

Description

Checks for the presence of labels and returns defaults

Usage

.makeLabels(
  x,
  labels,
  pattern = ".(fast|fq|bam|sam|cram).*",
  col = "Filename",
  ...
)

Arguments

x	A data.frame with a column titled "Filename"
labels	Named vector of labels for plotting
pattern	character Regular expression to remove from filenames
col	character Column to use for generating labels
...	Not used

Details

Takes a named vector of labels and checks for the correct fields. If no vector is supplied, returns the file names missing the specified pattern, which defaults to removing the suffixes fastq(.gz), fq(.gz), bam, sam or cram.

Value

Named character vector

Examples

f <- paste0(c("File1", "File2"), ".fastq")
df <- data.frame(Filename = f, stringsAsFactors = FALSE)
ngsReports:::.makeLabels(df)

UofABioinformaticsHub/fastqcReports documentation built on July 23, 2024, 3:26 p.m.