unmapped.genes: sgRNAs without reads

In caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

Description

CaRpools also provides you with the number of missing sgRNA, that means sgRNAs without a single read during NGS. If you want to know WHICH sgRNAs dropped out for a given gene, please consider using 'genes' as an optional argument with the gene identifier of interest.

Usage

unmapped.genes(data, namecolumn=1, fullmatchcolumn=2,
genes=NULL, extractpattern=expression("^(.+?)_.+"))

Arguments

data	A data.frame as created by 'load.file'. *Default* empty *Values* read-count data.frame
namecolumn	In which column are the sgRNA identifiers? *Default* 1 *Values* column number (numeric)
fullmatchcolumn	In which column are the read counts? *Default* 2 *Values* column number (numeric)
genes	If you want to know how many sgRNAs are not present for a single gene, set 'genes' to your gene identifier of interest. *Default* NULL *Values* gene identifier (character)
extractpattern	PERL regular expression that is used to retrieve the gene identifier from the overall sgRNA identifier. e.g. in **AAK1_107_0** it will extract **AAK1**, since this is the gene identifier beloning to this sgRNA identifier. **Please see: Read-Count Data Files** *Default* expression("^(.+?)(_.+)"), will work for most available libraries. *Values* PERL regular expression with parenthesis indicating the gene identifier (expression)

Value

Tabular output with number of missing sgRNAs for each gene or the name of the missing sgRNA if genes!=NULL.

Author(s)

Jan Winter

Examples

data(caRpools)
U1.unmapped = unmapped.genes(data=CONTROL1, namecolumn=1,
fullmatchcolumn=2, genes=NULL, extractpattern=expression("^(.+?)_.+"))

knitr::kable(U1.unmapped)

U1.unmapped = unmapped.genes(data=CONTROL1, namecolumn=1,
fullmatchcolumn=2, genes="random", extractpattern=expression("^(.+?)_.+"))

knitr::kable(U1.unmapped)

caRpools documentation built on May 2, 2019, 11:26 a.m.