CellTagExtraction: CellTag Extraction Function

Description Usage Arguments Value Examples

View source: R/CellTagExtraction_Function.R

Description

This function extracts CellTags from the raw fastq/bam sequencing file. If it is a fastq file, provides counts of each CellTag and sorts them in desending order. If it is a bam file, returns the barcode, umi, celltag information.

Usage

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CellTagExtraction(fastq.bam.input, celltag.version,
  extraction.output.filename, save.fullTag = TRUE, save.onlyTag = TRUE)

Arguments

fastq.bam.input

The input fastq/bam data directory

extraction.output.filename

The output file directory, i.e. where would you like to store the 8nt tags with their counts?

save.fullTag

Would you like to save full sequences with the short sequences provided without counts? Defaults to TRUE

save.onlyTag

Would you like to save only the 8nt CellTags without counts? Defaults to TRUE

short.nt.before.tag

A short sequence before the 8nt tag to help more specific identification

short.nt.after.tag

A short sequence after the 8nt tag to help more specific identification

Value

A list contains count table of CellTags. If requested to save fullTag counts, i.e. save.fullTag.counts = TRUE, return a list of both 8nt tags and full sequences count. Otherwise, a list of 8nt tags counts.

Examples

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CellTagExtraction("data.fastq", "v1", "~/Desktop/whitelist.txt")

morris-lab/CloneHunter documentation built on Jan. 6, 2019, 3:04 a.m.