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
)

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 bigstatsr::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