readProcessIsoloci {polyRAD}

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