X.snp.matrix-class {snpMatrix} | R Documentation |
This class extends the snp.matrix-class
to
deal with SNPs on the X chromosome.
Objects can be created by calls of the form new("X.snp.matrix", x,
Female)
.
Such objects have an additional slot
to objects of class
"snp.matrix"
consisting of a logical array of the same length as the number of
rows. This array indicates whether the sample corresponding to that row
came from a female (TRUE
) or a male (FALSE
).
.Data
:"matrix"
and storage mode
"raw"
Female
:"logical"
indicating
sex of samples
Class "snp.matrix"
, directly, with explicit coerce.
Class "matrix"
, by class "snp.matrix"
.
Class "structure"
, by class "snp.matrix"
.
Class "array"
, by class "snp.matrix"
.
Class "vector"
, by class "snp.matrix", with explicit coerce.
Class "vector"
, by class "snp.matrix", with explicit coerce.
signature(x = "X.snp.matrix")
: subset
operationssignature(x = "X.snp.matrix")
: subset
assignment operation to replace part of an objectsignature(from = "X.snp.matrix", to =
"character")
: map to codes 0, 1, 2, or NAsignature(from = "snp.matrix", to =
"X.snp.matrix")
:
maps a snp.matrix to an X.snp.matrix. Sex is inferred from the
genotype data since males should not be heterozygous at any locus.
After inferring sex, heterozygous calls for males are set to
NA
signature(object = "X.snp.matrix")
: map to codes
"A/A", "A/B", "B/B", "A/Y", "B/Y" or ""signature(object = "X.snp.matrix")
: returns
the sex distribution, together with
summaries of the data frames returned by
row.summary
and col.summary
David Clayton david.clayton@cimr.cam.ac.uk
http://www-gene.cimr.cam.ac.uk/clayton
X.snp-class
, snp.matrix-class
,
snp-class
data(testdata) summary(Xchromosome)