Extract variants from mutliple objects — extract

Chooses the correct function to extract variants from input based on the class of the object or the file extension. Different types of objects can be mixed within the list. For example, the list can include VCF files and maf objects. Certain parameters such as id and rename only apply to VCF objects or files and need to be individually specified for each VCF. Therefore, these parameters should be suppied as a vector that is the same length as the number of inputs. If other types of objects are in the input list, then the value of id and rename will be ignored for these items.

extract_variants(
  inputs,
  id = NULL,
  rename = NULL,
  sample_field = NULL,
  filename_as_id = FALSE,
  strip_extension = c(".vcf", ".vcf.gz", ".gz"),
  filter = TRUE,
  multiallele = c("expand", "exclude"),
  fix_vcf_errors = TRUE,
  extra_fields = NULL,
  chromosome_col = "chr",
  start_col = "start",
  end_col = "end",
  ref_col = "ref",
  alt_col = "alt",
  sample_col = "sample",
  verbose = TRUE
)

Arguments

inputs	A vector or list of objects or file names. Objects can be CollapsedVCF, ExpandedVCF, MAF, an object that inherits from `matrix` or `data.frame`, or character strings that denote the path to a vcf or maf file.
id	A character vector the same length as `inputs` denoting the sample to extract from a vcf. See `extract_variants_from_vcf` for more details. Only used if the input is a vcf object or file. Default `NULL`.
rename	A character vector the same length as `inputs` denoting what the same will be renamed to. See `extract_variants_from_vcf` for more details. Only used if the input is a vcf object or file. Default `NULL`.
sample_field	Some algoriths will save the name of the sample in the ##SAMPLE portion of header in the VCF. See `extract_variants_from_vcf` for more details. Default `NULL`.
filename_as_id	If set to `TRUE`, the file name will be used as the sample name. See `extract_variants_from_vcf_file` for more details. Only used if the input is a vcf file. Default `TRUE`.
strip_extension	Only used if `filename_as_id` is set to `TRUE`. If set to `TRUE`, the file extention will be stripped from the filename before setting the sample name. See `extract_variants_from_vcf_file` for more details. Only used if the input is a vcf file. Default `c(".vcf",".vcf.gz",".gz")`
filter	Exclude variants that do not have a `PASS` in the `FILTER` column of VCF inputs.
multiallele	Multialleles are when multiple alternative variants are listed in the same row in the vcf. See `extract_variants_from_vcf` for more details. Only used if the input is a vcf object or file. Default `"expand"`.
fix_vcf_errors	Attempt to automatically fix VCF file formatting errors. See `extract_variants_from_vcf_file` for more details. Only used if the input is a vcf file. Default `TRUE`.
extra_fields	Optionally extract additional fields from all input objects. Default `NULL`.
chromosome_col	The name of the column that contains the chromosome reference for each variant. Only used if the input is a matrix or data.frame. Default `"Chromosome"`.
start_col	The name of the column that contains the start position for each variant. Only used if the input is a matrix or data.frame. Default `"Start_Position"`.
end_col	The name of the column that contains the end position for each variant. Only used if the input is a matrix or data.frame. Default `"End_Position"`.
ref_col	The name of the column that contains the reference base(s) for each variant. Only used if the input is a matrix or data.frame. Default `"Tumor_Seq_Allele1"`.
alt_col	The name of the column that contains the alternative base(s) for each variant. Only used if the input is a matrix or data.frame. Default `"Tumor_Seq_Allele2"`.
sample_col	The name of the column that contains the sample id for each variant. Only used if the input is a matrix or data.frame. Default `"sample"`.
verbose	Show progress of variant extraction. Default `TRUE`.

Value

Returns a data.table of variants from a vcf

Examples

# Get loations of two vcf files and a maf file
luad_vcf_file <- system.file("extdata", "public_LUAD_TCGA-97-7938.vcf",
package = "musicatk")
lusc_maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
package = "musicatk")
melanoma_vcfs <- list.files(system.file("extdata", package = "musicatk"),
  pattern = glob2rx("*SKCM*vcf"), full.names = TRUE)

# Read all files in at once
inputs <- c(luad_vcf_file, melanoma_vcfs, lusc_maf_file)
variants <- extract_variants(inputs = inputs)
#> 
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  |==============                                                        |  20%
#> Extracted 1 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_LUAD_TCGA-97-7938.vcf
#> 
  |                                                                            
  |============================                                          |  40%
#> Extracted 2 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf
#> 
  |                                                                            
  |==========================================                            |  60%
#> Extracted 3 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf
#> 
  |                                                                            
  |========================================================              |  80%
#> Extracted 4 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf
#> 
  |                                                                            
  |======================================================================| 100%
#> Extracted 5 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_TCGA.LUSC.maf
table(variants$sample)
#> 
#> TCGA-97-7938-01A-11D-2167-08 TCGA-EE-A3J5-06A-11D-A20D-08 
#>                          121                          123 
#> TCGA-ER-A197-06A-32D-A197-08 TCGA-ER-A19O-06A-11D-A197-08 
#>                           13                           52 
#> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 
#>                          199                          283 
#> TCGA-94-7557-01A-11D-2122-08 
#>                          120 

# Run again but renaming samples in first four vcfs
new_name <- c(paste0("Sample", 1:4), NA)
variants <- extract_variants(inputs = inputs, rename = new_name)
#> 
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  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
#> Extracted 1 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_LUAD_TCGA-97-7938.vcf
#> 
  |                                                                            
  |============================                                          |  40%
#> Extracted 2 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf
#> 
  |                                                                            
  |==========================================                            |  60%
#> Extracted 3 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf
#> 
  |                                                                            
  |========================================================              |  80%
#> Extracted 4 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf
#> 
  |                                                                            
  |======================================================================| 100%
#> Extracted 5 out of 5 inputs: /private/var/folders/8g/zr_0d8wd23762jsqlwm5r_6w0000gn/T/RtmpqEjdyu/temp_libpathfbd337016ff7/musicatk/extdata/public_TCGA.LUSC.maf
table(variants$sample)
#> 
#>                      Sample1                      Sample2 
#>                          121                          123 
#>                      Sample3                      Sample4 
#>                           13                           52 
#> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 
#>                          199                          283 
#> TCGA-94-7557-01A-11D-2122-08 
#>                          120