Queries the provided regions and produces a matrix along with genomic
positions.
Parallelized across files using threads from the "iscream.threads" option.
Usage
make_mat(
bedfiles,
regions,
column,
mat_name = "value",
sparse = FALSE,
prealloc = 10000,
nthreads = NULL
)Arguments
- bedfiles
A vector of bedfile paths
- regions
A vector, data frame or GenomicRanges of genomic regions. See details.
- column
The index of the data column needed for the matrix
- mat_name
What to name the matrix in the returned list
- sparse
Whether to return a sparse matrix
- prealloc
The number of rows to initialize the matrices with. If the number of loci are approximately known, this can reduce runtime as fewer resizes need to be made.
- nthreads
Set number of threads to use overriding the
"iscream.threads"option. See?set_threadsfor more information.
Value
A named list of
the matrix with the value of interest
a character vector of chromosomes and numeric vector of base positions
a character vector of the input sample BED file names
Details
The input regions may be string vector in the form "chr:start-end" or a GRanges object. If a data frame is provided, they must have "chr", "start", and "end" columns.
Examples
bedfiles <- system.file("extdata", package = "iscream") |>
list.files(pattern = "[a|b|c|d].bed.gz$", full.names = TRUE)
# examine the bedfiles
colnames <- c("chr", "start", "end", "beta", "coverage")
lapply(bedfiles, function(i) knitr::kable(read.table(i, col.names = colnames)))
#> [[1]]
#>
#>
#> |chr | start| end| beta| coverage|
#> |:----|-----:|---:|----:|--------:|
#> |chr1 | 0| 2| 1.0| 1|
#> |chr1 | 2| 4| 1.0| 1|
#> |chr1 | 4| 6| 0.0| 2|
#> |chr1 | 6| 8| 0.0| 1|
#> |chr1 | 8| 10| 0.5| 2|
#> |chr1 | 10| 12| 1.0| 2|
#> |chr1 | 12| 14| 1.0| 3|
#>
#> [[2]]
#>
#>
#> |chr | start| end| beta| coverage|
#> |:----|-----:|---:|----:|--------:|
#> |chr1 | 0| 2| 0| 2|
#> |chr1 | 4| 6| 1| 2|
#> |chr1 | 6| 8| 1| 1|
#> |chr1 | 10| 12| 0| 2|
#> |chr1 | 12| 14| 1| 1|
#>
#> [[3]]
#>
#>
#> |chr | start| end| beta| coverage|
#> |:----|-----:|---:|----:|--------:|
#> |chr1 | 2| 4| 1| 2|
#> |chr1 | 6| 8| 0| 2|
#> |chr1 | 8| 10| 1| 1|
#>
#> [[4]]
#>
#>
#> |chr | start| end| beta| coverage|
#> |:----|-----:|---:|----:|--------:|
#> |chr1 | 0| 2| 1.0| 1|
#> |chr1 | 2| 4| 1.0| 2|
#> |chr1 | 6| 8| 0.0| 1|
#> |chr1 | 8| 10| 0.5| 2|
#> |chr1 | 12| 14| 1.0| 1|
#>
# make a vector of regions
regions <- c("chr1:1-6", "chr1:7-10", "chr1:11-14")
# make matrix of beta values
make_mat(bedfiles, regions, column = 4)
#> [17:51:28.368471] [iscream::query_all] [info] Querying 3 regions from 4 bedfiles
#>
#> [17:51:28.368863] [iscream::query_all] [info] Creating metadata vectors
#> [17:51:28.368895] [iscream::query_all] [info] 7 loci found - 9993 extra rows allocated with 0 resizes
#> [17:51:28.368900] [iscream::query_all] [info] Creating dense matrix
#> $value
#> a b c d
#> [1,] 1.0 0 0 1.0
#> [2,] 1.0 0 1 1.0
#> [3,] 0.0 1 0 0.0
#> [4,] 0.0 1 0 0.0
#> [5,] 0.5 0 1 0.5
#> [6,] 1.0 0 0 0.0
#> [7,] 1.0 1 0 1.0
#>
#> $pos
#> [1] 0 2 4 6 8 10 12
#>
#> $chr
#> [1] "chr1" "chr1" "chr1" "chr1" "chr1" "chr1" "chr1"
#>
#> $sampleNames
#> [1] "a" "b" "c" "d"
#>