create_indel_mutation_catalogue_from_df {YAPSA} | R Documentation |
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)
create_indel_mutation_catalogue_from_df( in_dat, in_signature_df, in_REF.field = "REF", in_ALT.field = "ALT", in_verbose = FALSE )
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
( |
in_signature_df |
A numeric data frame |
in_REF.field |
String indicating which column of |
in_ALT.field |
String indicating which column of |
in_verbose |
Verbose if |
A dataframe in the format of a mutational catalog V
, which can
be used for LCD
analysis
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)