From 479741fac5497d94b8bedd0f0ff212f9aa1ba826 Mon Sep 17 00:00:00 2001 From: Kristena Daley Date: Wed, 3 Nov 2021 13:35:26 -0700 Subject: [PATCH] update function to accept maf and seg file paths --- R/utilities.R | 29 +++++++++++++++++++++-------- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/R/utilities.R b/R/utilities.R index 04278b2f..aa72601d 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -901,8 +901,11 @@ collate_curated_sv_results = function(sample_table){ #' #' @examples #' cn_list = assign_cn_to_ssm(this_sample="HTMCP-01-06-00422-01A-01D",coding_only=TRUE) -assign_cn_to_ssm = function(this_sample,coding_only=FALSE,from_flatfile=FALSE, - use_augmented_maf=FALSE){ +assign_cn_to_ssm = function(this_sample,coding_only=FALSE, + from_flatfile=FALSE, + use_augmented_maf=FALSE, + maf_file, + seg_file){ database_name = config::get("database_name") project_base = config::get("project_base") @@ -911,7 +914,10 @@ assign_cn_to_ssm = function(this_sample,coding_only=FALSE,from_flatfile=FALSE, #project_base = "/projects/nhl_meta_analysis_scratch/gambl/results_local/" coding_class = c("Frame_Shift_Del","Frame_Shift_Ins","In_Frame_Del","In_Frame_Ins","Missense_Mutation","Nonsense_Mutation","Nonstop_Mutation","Splice_Region","Splice_Site","Targeted_Region","Translation_Start_Site") - if(from_flatfile){ + if(!missing(maf_file)){ + maf_sample = fread_maf(maf_file) %>% + dplyr::mutate(Chromosome = gsub("chr","",Chromosome)) + }else if(from_flatfile){ #get the genome_build for this sample bam_info = get_bams(this_sample) #message(paste("bams:",bam_info)) @@ -952,7 +958,18 @@ assign_cn_to_ssm = function(this_sample,coding_only=FALSE,from_flatfile=FALSE, maf_sample = dplyr::filter(maf_sample,Variant_Classification %in% coding_class) } #if(tool_name == "battenberg"){ - if(from_flatfile){ + + if(!missing(seg_file)){ + seg_sample = read_tsv(seg_file) %>% + dplyr::mutate(size=end - start) %>% + dplyr::filter(size > 100) + colnames(seg_sample)[c(1:4)] = c("ID","chrom","start","end") + seg_sample = seg_sample %>% + dplyr::mutate(chrom = gsub("chr","",chrom)) %>% + dplyr::rename(Chromosome=chrom,Start_Position=start,End_Position=end) %>% + data.table::as.data.table() + print(seg_sample) + }else if(from_flatfile){ message(paste("fetching:",tool_name)) battenberg_files = fetch_output_files(build=genome_build,base_path = "gambl/battenberg_current",tool="battenberg",search_pattern = ".igv.seg") @@ -998,10 +1015,6 @@ assign_cn_to_ssm = function(this_sample,coding_only=FALSE,from_flatfile=FALSE, geom_segment(data=seg_sample,aes(x=Start_Position,xend=End_Position,y=CN,yend=CN,colour=LOH_flag)) + facet_wrap(~Chromosome,scales="free_x") return(list(maf=a,seg=seg_sample)) - if(!from_flatfile){ - DBI::dbDisconnect(con) - } - }