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Make a matrix from a numeric column of BED files

Source: R/make_mat.R
make_mat.Rd

Queries the provided regions and produces a matrix along with genomic positions as a named list (make_mat()), a RangedSummarizedExperiment (make_mat_se()), GRanges (make_mat_gr()). 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
)

make_mat_se(
  bedfiles,
  regions,
  column,
  mat_name = "value",
  sparse = FALSE,
  prealloc = 10000,
  nthreads = NULL
)

make_mat_gr(
  bedfiles,
  regions,
  column,
  mat_name = "value",
  prealloc = 10000,
  nthreads = NULL
)

Arguments

bedfiles

A vector of BED file 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 object

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 the number of threads to use. Overrides the "iscream.threads" option. See ?set_threads for more information.

Value

  • make_mat(): 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

  • make_mat_gr(): if GenomicRanges is available, a GRanges

  • make_mat_se(): if SummarizedExperiment is available, a RangedSummarizedExperiment

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)
#> [15:51:51.947510] [iscream::query_all] [info] Querying 3 regions from 4 bedfiles
#> 
#> [15:51:51.947926] [iscream::query_all] [info] Creating metadata vectors
#> [15:51:51.947959] [iscream::query_all] [info] 7 loci found - 9993 extra rows allocated with 0 resizes
#> [15:51:51.947963] [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"
#>