Count Tryptase Alleles in a .sam File

Usage

count_tryptase(sam_file)

Arguments

sam_file: path to the temp.sam file generated by the pre-processing

Value

A vector of counts suitable for input to TrpLik. See Details.

Details

The first four of values are the numbers of reads mapping uniquely to ⍺, βI, βII or βIII alleles in the specific 83 bp region where all four alleles can be distinguished from each other.

The next two are the numbers of reads that map uniquely to β ‘wildtype’ (i.e. not frameshifted) and β frameshifted sequences.

The final three are the numbers of reads that can be uniquely mapped to ⍺, β, or δ alleles respectively.

Examples

if (FALSE) { # \dontrun{
count_tryptase("temp.sam")
} # }