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#' create_bed_file
#'
#' Creates BED files from the found and not found annotated mutations
#'
#' @param match_t R table which contains the mutations from the
#' training database for the cancer cell lines
#' @param vcf_fingerprint contains the mutations that are present
#' in the query cancer cell line's vcf file
#' @param output_file Path to output file
#' @param ref_gen Reference genome version
#' @param manual_identifier Manually enter a vector of CL name(s)
#' whose bed files should be created, independently from them
#' passing the detection threshold
#' @return Returns a message which indicates if the BED file
#' creation has succeeded
#' @usage
#' create_bed_file(
#' match_t,
#' vcf_fingerprint,
#' output_file,
#' ref_gen,
#' manual_identifier
#'
#' )
create_bed_file = function(
match_t,
vcf_fingerprint,
output_file,
ref_gen,
manual_identifier
){
# prep
# start
print("Creating bed files")
found_res_tab = res_table[ as.logical( res_table$Conf_score_sig ), ]
found_identifier = paste(
found_res_tab$CL, found_res_tab$CL_source, sep = "_"
)
found_identifier = unique( c( manual_identifier, found_identifier ) )
for ( identifier in found_identifier ){
if ( identifier != "" ){
print(identifier)
name_training_bed_file = stringr::str_replace(
output_file,
"_uniquorn_ident.tab",
paste0(
c(
"_uniquorn_ident_mutations_reference_variants_",
identifier,
".bed"
),
collapse = ""
)
)
name_query_bed_file = stringr::str_replace(
output_file, "_uniquorn_ident.tab",
paste0(
c(
"_uniquorn_ident_mutations_query_variants_",
identifier,
".bed"
),
collapse = ""
)
)
name_missed_bed_file = stringr::str_replace(
output_file,
"_uniquorn_ident.tab",
paste0(
c(
"_uniquorn_ident_mutations_non_matching_variants_",
identifier,
".bed"
),
collapse = ""
)
)
# training
training_bed_file = paste0(
c(
'track name=',
'Training_',
identifier,
' description=Variants_in_reference type=bedDetail db=',
ref_gen,
' color=0,0,255 priority=3'
),
collapse = ""
)
training_coords = sim_list$Fingerprint[ sim_list$CL == identifier ]
training_coords = stringr::str_trim( training_coords )
training_coords = training_coords[
!grepl("^[c(']", training_coords)]
training_coords = stringr::str_split( training_coords, "_" )
training_coords_res = sapply(training_coords,
FUN = function( vec ){
chrom = paste( "chr", stringr::str_trim(vec[1]), sep = "" )
return(
paste0(
c(
chrom,
as.character(
as.integer(
vec[2]
) - 1
),
as.integer(
as.integer(
vec[3]
)
)
),
collapse = "\t"
)
)
}
)
training_coords_res = c(
training_bed_file,
training_coords_res
)
utils::write.table(
x = training_coords_res,
file = name_training_bed_file,
sep ="",
row.names = FALSE,
col.names = FALSE,
quote = FALSE
)
# query
query_bed_file = paste0(
c(
'track name=',
'Query_',
identifier,
' description=Variants_in_query type=bedDetail db=',
ref_gen,
' color=0,255,0 priority=3'
),
collapse = ""
)
query_coords = vcf_fingerprint
query_coords = stringr::str_trim( query_coords )
query_coords = query_coords[ ! grepl("^[c(']", query_coords ) ]
query_coords = stringr::str_split( query_coords, "_" )
query_coords_res = sapply( query_coords, FUN = function( vec ){
chrom = paste( "chr", stringr::str_trim( vec[1] ), sep = "" )
return(
paste0(
c(
chrom,
as.character(
as.integer(
vec[2]
) - 1
),
as.integer(
as.integer(
vec[3]
)
)
),
collapse = "\t"
)
)
} )
query_res = c( query_bed_file, query_coords_res )
utils::write.table(
x = query_res,
file = name_query_bed_file,
sep = "",
row.names = FALSE,
col.names = FALSE,
quote = FALSE
)
# missed
missed_bed_file = paste0(
c(
'track name=',
'Missed_',
identifier,
' description=Non_matching_variants type=bedDetail db=',
ref_gen,
' color=255,0,0 priority=3'
),
collapse = ""
)
missed_coords = training_coords[
which( ! ( training_coords %in% query_coords ) ) ]
missed_coords = sapply( missed_coords, FUN = function( vec ){
chrom = paste( "chr", stringr::str_trim( vec[1] ), sep = "" )
return(
paste0(
c(
chrom,
as.character(
as.integer(
vec[2]
) -1
),
as.integer(
as.integer(
vec[3]
)
)
),
collapse = "\t"
)
)
})
missed_coords_res = c( missed_bed_file, missed_coords )
utils::write.table(
x = missed_coords_res,
file = name_missed_bed_file,
sep = "",
row.names = FALSE,
col.names = FALSE,
quote = FALSE
)
}
}
}
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