VariantExperiment-methods {VariantExperiment} | R Documentation |
VariantExperiment
objects.Statistical functions for VariantExperiment
objects.
## S4 method for signature 'VariantExperiment' seqAlleleFreq( gdsfile, ref.allele = 0L, minor = FALSE, .progress = FALSE, parallel = seqGetParallel(), verbose = FALSE ) ## S4 method for signature 'VariantExperiment' seqAlleleCount( gdsfile, ref.allele = 0L, minor = FALSE, .progress = FALSE, parallel = seqGetParallel(), verbose = FALSE ) ## S4 method for signature 'VariantExperiment' seqMissing( gdsfile, per.variant = TRUE, .progress = FALSE, parallel = seqGetParallel(), verbose = FALSE ) ## S4 method for signature 'VariantExperiment' seqNumAllele(gdsfile) ## S4 method for signature 'VariantExperiment' hwe(gdsobj, permute = FALSE) ## S4 method for signature 'VariantExperiment' inbreedCoeff(gdsobj, margin = c("by.variant", "by.sample"), use.names = FALSE) ## S4 method for signature 'VariantExperiment' pca(gdsobj, eigen.cnt = 32) ## S4 method for signature 'VariantExperiment' titv(gdsobj, by.sample = FALSE, use.names = FALSE) ## S4 method for signature 'VariantExperiment' refDosage(gdsobj, use.names = TRUE) ## S4 method for signature 'VariantExperiment' altDosage(gdsobj, use.names = TRUE, sparse = FALSE) ## S4 method for signature 'VariantExperiment' countSingletons(gdsobj, use.names = FALSE) ## S4 method for signature 'VariantExperiment' heterozygosity( gdsobj, margin = c("by.variant", "by.sample"), use.names = FALSE ) ## S4 method for signature 'VariantExperiment' homozygosity( gdsobj, allele = c("any", "ref", "alt"), margin = c("by.variant", "by.sample"), use.names = FALSE ) ## S4 method for signature 'VariantExperiment' meanBySample(gdsobj, var.name, use.names = FALSE) ## S4 method for signature 'VariantExperiment' isSNV(gdsobj, biallelic = TRUE) ## S4 method for signature 'VariantExperiment' isVariant(gdsobj, use.names = FALSE)
gdsfile |
an |
ref.allele |
a single numeric value, a numeric vector or a
character vector; see |
minor |
if ‘TRUE’, return minor allele frequency/count |
.progress |
Logical, show process information if |
parallel |
A logical value to indicate serial processing
( |
verbose |
if ‘TRUE’, show progress information |
per.variant |
A logical value to indicate whether to calculate
missing rate for variant ( |
gdsobj |
same as above |
permute |
A logical value indicating whether to permute the
genotypes. See |
margin |
"by.variant" OR "by.sample" to indicate
whether the calculation should be done over all samples for
each variant, or over all variants for each sample. See
|
use.names |
A logical value indicating whether to assign variant or sample IDs as names of the output vector. |
eigen.cnt |
An integer value indicating how many eigenvalues and eignvectors to return. The default is 32. |
by.sample |
A logical value indicating whether TiTv should be
calculated by sample or overall for the entire
|
sparse |
A Logical value indicating whether or not to return
the alterate allele dosage as a sparse matrix. In most cases,
it will dramatically reduce the size of the returned
object. See |
allele |
Choose from "any", "ref," or "alt," to indicate which
alleles to consider when calculating homozygosity. See
|
var.name |
Character string with name of the variable. Choose
from |
biallelic |
A logical indicating whether to only consider
biallelic SNVs. See |
Statistical results in vector
or data.frame
format.
gds <- SeqArray::seqExampleFileName("gds") ## ve <- makeVariantExperimentFromGDS(gds) ## ve ## sample missing rate ## mr.samp <- seqMissing(ve, per.variant = FALSE) ## ead(mr.samp) ## hwe ## hwe <- hwe(ve) ## head(hwe) ## titv ratio by sample / overall ## titv <- titv(ve, by.sample=TRUE) ## head(titv) ## titv(ve, by.sample=FALSE) ## countSingletons ## countSingletons(ve)