AlleleProfileR.summary.profiled.alleles: Summary statistics of the profiled alleles

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function generates summary statistics of the profiled alleles of a sample.

Usage

AlleleProfileR.summary.profiled.alleles(profiledvariants, cutoff = 0,
  ignore.single = F, top = 0, alternateallele = NULL)

Arguments

profiledvariants	Variants data.frame, as defined by AlleleProfileR.determine.variants.
cutoff	Percent value (0 to 1), representing the treshold read count for a certain allelic variant to be included in further analysis.
ignore.single	Ingore alleles representing a single read pair? Default is FALSE.
top	Only report the top x variants
alternateallele	Alternate allele name

Value

Detailed summary table. Allele: allele name, count: read counts, qname: identifier of a representative read, wt: wild type coding sequence, snp: no of SNPs, atg: ATG destroyed, coding: coding for a protein, coding length: length of the exon, fs: frame shift present, stop: stop destroyed, pstop: premature stop inserted, sm: small indel, lg: large indel, utr: indel in UTR region, cryptic: cryptic coding frame present, error: errors in analysis, seq: read sequence, cdsseq: coding frame sequence, pos: start position, cigar: cigar string, indelseq: indel sequences.

Author(s)

Arne Bruyneel

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.