seqBlockApply {SeqArray} | R Documentation |
Returns a vector or list of values obtained by applying a function to margins of genotypes and annotations via blocking.
seqBlockApply(gdsfile, var.name, FUN, margin=c("by.variant"), as.is=c("none", "list", "unlist"), var.index=c("none", "relative", "absolute"), bsize=1024L, parallel=FALSE, .useraw=FALSE, .progress=FALSE, ...)
gdsfile |
a |
var.name |
the variable name(s), see details |
FUN |
the function to be applied |
margin |
giving the dimension which the function will be applied over |
as.is |
returned value: a list, a vector or none;
|
var.index |
if |
bsize |
block size |
parallel |
|
.useraw |
|
.progress |
if |
... |
optional arguments to |
The variable name should be "sample.id"
, "variant.id"
,
"position"
, "chromosome"
, "allele"
, "genotype"
,
"annotation/id"
, "annotation/qual"
, "annotation/filter"
,
"annotation/info/VARIABLE_NAME"
, or
"annotation/format/VARIABLE_NAME"
.
"@genotype"
, "annotation/info/@VARIABLE_NAME"
or
"annotation/format/@VARIABLE_NAME"
are used to obtain the index
associated with these variables.
"$dosage"
is also allowed for the dosages of reference allele (integer:
0, 1, 2 and NA for diploid genotypes).
"$dosage_alt"
returns a RAW/INTEGER matrix for the dosages of alternative
allele without distinguishing different alternative alleles.
"$num_allele"
returns an integer vector with the numbers of distinct
alleles.
"$ref"
returns a character vector of reference alleles
"$alt"
returns a character vector of alternative alleles (delimited by
comma)
"$chrom_pos"
returns characters with the combination of chromosome and
position, e.g., "1:1272721". "$chrom_pos_allele"
returns characters with
the combination of chromosome, position and alleles, e.g., "1:1272721_A_G"
(i.e., chr:position_REF_ALT).
The algorithm is highly optimized by blocking the computations to exploit the high-speed memory instead of disk.
A vector, a list of values or none.
Xiuwen Zheng
seqApply
, seqSetFilter
,
seqGetData
, seqParallel
,
seqGetParallel
# the GDS file (gds.fn <- seqExampleFileName("gds")) # display (f <- seqOpen(gds.fn)) # get 'sample.id (samp.id <- seqGetData(f, "sample.id")) # "NA06984" "NA06985" "NA06986" ... # get 'variant.id' head(variant.id <- seqGetData(f, "variant.id")) # set sample and variant filters set.seed(100) seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)], variant.id=sample(variant.id, 10)) # read seqApply(f, "genotype", FUN=print, margin="by.variant") seqApply(f, "genotype", FUN=print, margin="by.variant", .useraw=TRUE) seqApply(f, "genotype", FUN=print, margin="by.sample") seqApply(f, "genotype", FUN=print, margin="by.sample", .useraw=TRUE) # read in block seqGetData(f, "$dosage") seqBlockApply(f, "$dosage", print, bsize=3) seqBlockApply(f, "$dosage", function(x) x, as.is="list", bsize=3) seqBlockApply(f, c(dos="$dosage", pos="position"), print, bsize=3) # close the GDS file seqClose(f)