bed_counts {bigsnpr} | R Documentation |
Counts
Description
Counts the number of 0s, 1s, 2s and NAs by variants in the bed file.
Usage
bed_counts(
obj.bed,
ind.row = rows_along(obj.bed),
ind.col = cols_along(obj.bed),
byrow = FALSE,
ncores = 1
)
Arguments
obj.bed |
Object of type bed, which is the mapping of some bed file.
Use |
ind.row |
An optional vector of the row indices (individuals) that
are used. If not specified, all rows are used. |
ind.col |
An optional vector of the column indices (SNPs) that are used.
If not specified, all columns are used. |
byrow |
Whether to count by individual rather than by variant?
Default is |
ncores |
Number of cores used. Default doesn't use parallelism. You may use nb_cores. |
Value
A matrix of with 4 rows and length(ind.col)
columns.
Examples
bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
obj.bed <- bed(bedfile)
bed_counts(obj.bed, ind.col = 1:5)
bed_counts(obj.bed, ind.row = 1:5, byrow = TRUE)
[Package bigsnpr version 1.12.2 Index]