readProcessIsoloci: Import Read Depth from Output of process_isoloci.py

In polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Import Read Depth from Output of process_isoloci.py

Description

After process_isoloci.py is used to assign RAD tags to alignment locations within a highly duplicated genome, readProcessIsoloci imports the resulting CSV to a "RADdata" object.

Usage

readProcessIsoloci(sortedfile, min.ind.with.reads = 200,
                   min.ind.with.minor.allele = 10,
                   min.median.read.depth = 10,
                   possiblePloidies = list(2), taxaPloidy = 2L,
                   contamRate = 0.001,
                   nameFromTagStart = TRUE, mergeRareHap = TRUE)

Arguments

sortedfile	File path to a CSV output by process_isoloci.py.
min.ind.with.reads	Minimum number of individuals with reads needed to retain a locus.
min.ind.with.minor.allele	Minimum number of individuals with reads in a minor allele needed to retain a locus.
min.median.read.depth	Minimum median read depth across individuals (including individuals with depth 0) needed to retain a locus.
possiblePloidies	A list indicating possible inheritance modes of loci. See RADdata.
taxaPloidy	A single integer, or an integer vector with one value per taxon, indicating ploidy. See RADdata.
contamRate	Approximate rate of cross-contamination among samples.
nameFromTagStart	If TRUE loci will be named based on the alignment position and strand of the RAD tag itself. If FALSE, loci will be named based on the leftmost position of the variable region of the RAD tag. In either case, locTable$Pos within the output will indicate the position of the variable region of the tag.
mergeRareHap	Boolean indicating whether to run MergeRareHaplotypes after building the "RADdata" object.

Details

MergeIdenticalHaplotypes is used internally by this function to merge alleles with identical sequence for the region shared by all tags, in cases where tags vary in length within a locus.

Value

A "RADdata" object containing read depth and alignment positions from sortedfile.

Author(s)

Lindsay V. Clark

See Also

readProcessSamMulti

polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.