Get ASHM Count Matrix.
get_ashm_count_matrix.RdPrepare a matrix with one row per sample and one column per region using a set of hypermutated regions.
Usage
get_ashm_count_matrix(
regions_bed,
these_samples_metadata,
this_seq_type,
projection = "grch37"
)Arguments
- regions_bed
A bed file with one row for each region.
- these_samples_metadata
This is used to complete your matrix. All GAMBL samples will be used by default. Provide a data frame with at least sample_id for all samples if you are using non-GAMBL data.
- this_seq_type
The seq type to return results for. Only used if no metadata is provided with these_samples_metadata.
- projection
Which genome build to use for the mutations (must match the coordinate system your regions to avoid a nonsense result)
Examples
regions_bed = create_bed_data(GAMBLR.data::grch37_ashm_regions,
fix_names="concat",
concat_cols=c("gene","region"),
sep="-")
my_meta = get_gambl_metadata() %>% dplyr::filter(pathology=="DLBCL")
#> Using the bundled metadata in GAMBLR.data...
shm_matrix <- get_ashm_count_matrix(
regions_bed = regions_bed,
this_seq_type = "genome",
these_samples_metadata = my_meta
)
#> Using the bundled SSM calls (.maf) calls in GAMBLR.data...
#> Using the bundled SSM calls (.maf) calls in GAMBLR.data...
#> id_ease: WARNING! 1783 samples in the provided metadata were removed because their seq types are not the same as in the `set_type` argument. Use `verbose = TRUE` to see their IDs.
#> Running in default mode of any...
#> Joining with `by = join_by(sample_id, region_name)`
head(shm_matrix[,c(1:12)])
#> AICDA-TSS BACH2-TSS BCL11A-TSS BCL2-TSS BCL2-intron BCL6-Intergenic-1
#> 02-13135T 0 1 0 20 0 0
#> 02-20170T 1 1 0 0 0 0
#> 02-22991T 0 0 0 0 0 0
#> 04-24937T 0 2 15 4 0 0
#> 04-28140T 0 0 0 0 0 0
#> 04-29264T 0 0 0 0 0 0
#> BCL6-Intergenic-2 BCL6-Intergenic-3 BCL6-Intergenic-4
#> 02-13135T 0 1 0
#> 02-20170T 0 2 0
#> 02-22991T 0 0 1
#> 04-24937T 0 1 0
#> 04-28140T 0 0 0
#> 04-29264T 0 2 2
#> BCL6-Intergenic-5 BCL6-TSS BCL7A-TSS
#> 02-13135T 0 4 3
#> 02-20170T 0 2 0
#> 02-22991T 0 1 0
#> 04-24937T 0 12 2
#> 04-28140T 0 0 0
#> 04-29264T 1 3 3
if (FALSE) { # \dontrun{
#this example should fail because the regions_bed is not hg38
shm_matrix <- get_ashm_count_matrix(regions_bed=regions_bed,
this_seq_type = "genome",
these_samples_metadata = my_meta,
projection = "hg38")
# Error in get_ashm_count_matrix(
# Your projection argument does not match the genome_build of regions_bed
} # }
# format the name column to include the coordinates instead of the gene
regions_bed = create_bed_data(GAMBLR.data::hg38_ashm_regions,
fix_names="concat",
concat_cols=c("chr_name","hg38_start","hg38_end"),
sep="-")
matrix_hg38 <- get_ashm_count_matrix(regions_bed=regions_bed,
this_seq_type = "genome",
these_samples_metadata = my_meta,
projection = "hg38")
#> Using the bundled SSM calls (.maf) calls in GAMBLR.data...
#> Using the bundled SSM calls (.maf) calls in GAMBLR.data...
#> id_ease: WARNING! 1783 samples in the provided metadata were removed because their seq types are not the same as in the `set_type` argument. Use `verbose = TRUE` to see their IDs.
#> Running in default mode of any...
#> Joining with `by = join_by(sample_id, region_name)`
print(dim(matrix_hg38))
#> [1] 2312 129
print(head(matrix_hg38[,c(1:8)]))
#> chr1-203305570-203306650 chr1-226732862-226740184
#> 02-13135T 0 0
#> 02-20170T 0 0
#> 02-22991T 0 0
#> 04-24937T 21 0
#> 04-28140T 0 0
#> 04-29264T 1 0
#> chr1-226733387-226740281 chr1-28506039-28509827
#> 02-13135T 0 0
#> 02-20170T 0 0
#> 02-22991T 0 0
#> 04-24937T 0 0
#> 04-28140T 0 0
#> 04-29264T 0 0
#> chr1-30756165-30759164 chr11-102317439-102319346
#> 02-13135T 0 0
#> 02-20170T 0 1
#> 02-22991T 0 0
#> 04-24937T 0 4
#> 04-28140T 0 0
#> 04-29264T 0 0
#> chr11-111377353-111379499 chr11-118883749-118885805
#> 02-13135T 0 0
#> 02-20170T 0 0
#> 02-22991T 0 0
#> 04-24937T 1 0
#> 04-28140T 0 0
#> 04-29264T 1 0