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.
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)A "RADdata" object containing read depth and alignment positions
from sortedfile.
File path to a CSV output by process_isoloci.py.
Minimum number of individuals with reads needed to retain a locus.
Minimum number of individuals with reads in a minor allele needed to retain a locus.
Minimum median read depth across individuals (including individuals with depth 0) needed to retain a locus.
A list indicating possible inheritance modes of loci. See RADdata.
A single integer, or an integer vector with one value per taxon, indicating
ploidy. See RADdata.
Approximate rate of cross-contamination among samples.
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.
Boolean indicating whether to run MergeRareHaplotypes after
building the "RADdata" object.
Lindsay V. Clark
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.
readProcessSamMulti