readProcessSamMulti | R Documentation |
This function imports the files output by process_sam_multi.py
to a
"RADdata"
object so that HindHe
can be run to
filter samples and determine optimal parameters for process_isoloci.py
.
readProcessSamMulti(alignfile, depthfile = sub("align", "depth", alignfile), expectedLoci = 1000, min.ind.with.reads = 200, min.ind.with.minor.allele = 10, possiblePloidies = list(2), taxaPloidy = 2L, contamRate = 0.001, expectedAlleles = expectedLoci * 15, maxLoci = expectedLoci)
alignfile |
A file output by |
depthfile |
A file output by |
expectedLoci |
The number of loci expected in the final object. The default, 1000, is fairly small because this function is intended to be used for preliminary analysis only. |
min.ind.with.reads |
The minimum number of taxa with reads needed in order for a locus to be retained in the output. |
min.ind.with.minor.allele |
The minimum number of taxa with the same minor allele needed in order for a locus to be retained in the output. |
possiblePloidies |
A list indicating expected inheritance modes for markers. See
|
taxaPloidy |
A single integer, or an integer vector with one value per taxon, indicating
ploidy. See |
contamRate |
A number ranging from zero to one (although in practice probably less than 0.01) indicating the expected sample cross-contamination rate. |
expectedAlleles |
The expected number of alleles in the dataset. |
maxLoci |
The maximum number of loci to import before ceasing to read the file. Set to
|
A "RADdata"
object.
Lindsay V. Clark
readProcessIsoloci
## Not run: myRAD <- readProcessSamMulti("mydata_2_align.csv") ## End(Not run)
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