create_indel_mutation_catalogue_from_df: Wrapper to create an INDEL mutational catalog from a vlf-like...

In YAPSA: Yet Another Package for Signature Analysis

Description

From data frame constucted from a vcf-file file the function create_indel_mutation_catalogue_from_df creates a mutational catalog V by squencially applying the attribute_sequence_contex_indel, attribute_sequence_contex_indel and then attribution_of_indels. The runtime of the function is about 1 sec per 6 variants as sequence context as well as INDEL calssification are timeconsuming to compute (optimization ongoing)

Usage

create_indel_mutation_catalogue_from_df(
  in_dat,
  in_signature_df,
  in_REF.field = "REF",
  in_ALT.field = "ALT",
  in_verbose = FALSE
)

Arguments

in_dat	A data frame constructed from a vcf-like file of a whole cohort or single-sample. The first columns are those of a standard vcf file (CHROM, POS, REF and ALT), followed by an arbitrary number of custom or used defined columns. One of these can carry a PID (patient or sample identifyier) and one can carry subgroup information.
in_signature_df	A numeric data frame W with n rows and l columns, n being the number of features and l being the number od signatures. Data frame containing INDEL signatures which should be used to create the mutational cataologe V.
in_REF.field	String indicating which column of in_dat carries the reference base if dealing with data frames
in_ALT.field	String indicating which column of in_dat carries the variant base if dealing with data frames
in_verbose	Verbose if in_verbose=1

Value

A dataframe in the format of a mutational catalog V, which can be used for LCD analysis

Examples

data(sigs_pcawg)
data(GenomeOfNl_raw)
temp_df <- translate_to_hg19(GenomeOfNl_raw[1:200,],"CHROM")
temp_df$PID <- sample(c("PID1","PID2","PID3","PID4","PID5"),200,replace=TRUE)
temp <- create_indel_mutation_catalogue_from_df(in_dat = temp_df,
   in_signature_df = PCAWG_SP_ID_sigs_df,
   in_REF.field = "REF",
   in_ALT.field = "ALT",
   in_verbose = FALSE)
dim(temp)
head(temp)

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.