Description Usage Arguments Value
View source: R/seqarray_process_helpers.R
Extract major alleles from a GDS file using the non-reference allele frequency (NRAF) estimated from read counts directly. In the case of RAF = 0.5 we select the major allele randomly from Bernoulli distribution if use.hets is FALSE. Other wise hets are coded as 3. If get.nucleotides is TRUE a character matrix is retruned with the alleles coded, otherwise if use.hets the allele is coded as N. Missing genotype calls are coded as X.
1 |
gdsfile |
a |
get.nucleotides |
FALSE logical indicating whether to replace allele with nucleotide bases |
use.hets |
FALSE logical indicating whether to code hets sepeartely |
a binary matrix or character matrix containing reference and alternate alleles
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