Calculate Mutation Frequency By Sliding Window.
calc_mutation_frequency_bin_region.RdCount the number of mutations in a sliding window across a region for all samples.
Usage
calc_mutation_frequency_bin_region(
region,
these_samples_metadata = NULL,
these_sample_ids = NULL,
this_seq_type = "genome",
maf_data = NULL,
projection = "grch37",
slide_by = 100,
window_size = 1000,
return_format = "long",
min_count_per_bin = 0,
return_count = TRUE,
drop_unmutated = FALSE,
...
)Arguments
- region
A string describing a genomic region in the "chrom:start-end" format. The region must be specified in this format OR as separate chromosome, start_pos, end_pos arguments.
- these_samples_metadata
Optional data frame containing a sample_id column. If not providing a maf file, seq_type is also a required column.
- these_sample_ids
Optional vector of sample IDs. Output will be subset to IDs present in this vector.
- this_seq_type
Optional vector of seq_types to include in heatmap. Default is "genome". Uses default seq_type priority for samples with >1 seq_type.
- maf_data
Optional maf data frame. Will be subset to rows where Tumor_Sample_Barcode matches provided sample IDs or metadata table. If not provided, maf data will be obtained with get_ssm_by_regions().
- projection
Specify which genome build to use. Required. Default grch37.
- slide_by
Slide size for sliding window. Default 100.
- window_size
Size of sliding window. Default 1000.
- return_format
Return format of mutations. Accepted inputs are "long" and "wide". Long returns a data frame of one sample ID/window per row. Wide returns a matrix with one sample ID per row and one window per column. Using the "wide" format will retain all samples and windows regardless of the drop_unmutated or min_count_per_bin parameters.
- min_count_per_bin
Minimum counts per bin, default is 0. Setting this greater than 0 will drop unmutated windows only when return_format is long.
- return_count
Boolean statement to return mutation count per window (TRUE) or binary mutated/unmutated status (FALSE). Default is TRUE.
- drop_unmutated
Boolean for whether to drop windows with 0 mutations. Only effective with "long" return format.
- ...
Any additional parameters.
Details
This function is called to return the mutation frequency for a given
region, either from a provided input maf data frame or from the GAMBL maf data.
Regions are specified with the region parameter. Alternatively, the region of
interest can also be specified by calling the function with chromosome,
start_pos, and end_pos parameters. This function operates on a single region.
To return a matrix of sliding window counts over multiple regions,
see calc_mutation_frequency_bin_regions.
Examples
myc_region = "8:128747680-128753674"
myc_mut_freq = calc_mutation_frequency_bin_region(region = myc_region,
slide_by = 10,
window_size = 10000)
#> Using the bundled metadata in GAMBLR.data...
#> processing bins of size 10000 across 5994 bp region
#> Using GAMBLR.data::get_ssm_by_region...
#> Using the bundled metadata in GAMBLR.data...
#> Joining with `by = join_by(sample_id)`
#> Joining with `by = join_by(window_start)`
dplyr::arrange(myc_mut_freq,desc(mutation_count))
#> # A tibble: 612,000 × 3
#> sample_id bin mutation_count
#> <chr> <chr> <int>
#> 1 BLGSP-71-26-00399-01A-01E 8_128747680 41
#> 2 BLGSP-71-26-00399-01A-01E 8_128747690 41
#> 3 BLGSP-71-26-00399-01A-01E 8_128747700 41
#> 4 BLGSP-71-26-00399-01A-01E 8_128747710 41
#> 5 BLGSP-71-26-00399-01A-01E 8_128747720 41
#> 6 BLGSP-71-26-00399-01A-01E 8_128747730 41
#> 7 BLGSP-71-26-00399-01A-01E 8_128747740 41
#> 8 BLGSP-71-26-00399-01A-01E 8_128747750 41
#> 9 BLGSP-71-26-00399-01A-01E 8_128747760 41
#> 10 BLGSP-71-26-00399-01A-01E 8_128747770 41
#> # ℹ 611,990 more rows