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
)

Arguments

obj.bed

Object of type bed, which is the mapping of some bed file. Use obj.bed <- bed(bedfile) to get this object.

ind.row

An optional vector of the row indices (individuals) that are used. If not specified, all rows are used.
Don't use negative indices.

ind.col

An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used.
Don't use negative indices.

byrow

Whether to count by individual rather than by variant? Default is FALSE (count by variant).

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)
#> [,1] [,2] [,3] [,4] [,5] #> 0 183 177 170 165 155 #> 1 8 16 21 26 39 #> 2 0 0 1 4 2 #> <NA> 9 7 8 5 4
bed_counts(obj.bed, ind.row = 1:5, byrow = TRUE)
#> [,1] [,2] [,3] [,4] [,5] #> 0 492 275 316 271 346 #> 1 0 211 157 94 98 #> 2 0 0 18 117 39 #> <NA> 8 14 9 18 17