Counts
Counts the number of 0s, 1s, 2s and NAs by variants in the bed file.
bed_counts( obj.bed, ind.row = rows_along(obj.bed), ind.col = cols_along(obj.bed), byrow = FALSE, ncores = 1 )
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. |
A matrix of with 4 rows and length(ind.col) columns.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.