Merge pull request #146 from sangeetashukla/update-gene-match

Fixed path in qc script, removed unwanted symbols from ensg mapping file
d3b-center · Oct 22, 2021 · 10fd9d5 · 10fd9d5
2 parents e94cf36 + 96f5124
commit 10fd9d5
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Showing 5 changed files with 46 additions and 43 deletions.
diff --git a/analyses/gene_match/add_pmtl_ens_hugo.Rmd b/analyses/gene_match/add_pmtl_ens_hugo.Rmd
@@ -37,5 +37,6 @@ ens_hugo_pmtl <- ens_map %>%
   full_join(pmtl) %>%
   select(ensg_id, gene_symbol, pmtl, version) %>%
   distinct() %>%
+  filter(!ensg_id == "Symbol_Not_Found" | !gene_symbol == 'NA') %>%
   write_tsv("results/ensg-hugo-pmtl-mapping.tsv")
 ```
diff --git a/analyses/gene_match/add_pmtl_ens_hugo.nb.html b/analyses/gene_match/add_pmtl_ens_hugo.nb.html
diff --git a/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.Rmd b/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.Rmd
@@ -14,7 +14,7 @@ suppressPackageStartupMessages({
 ## Read ensg-hugo-pmtl-mapping.tsv and OpenPedCan SNV, CNV, TPM, and fusion data
 
 ```{r read_open_ped_can_data}
-open_ped_can_data_path <- '~/OpenPedCan-analysis/data/v10'
+open_ped_can_data_path <- '../../data'
 
 snv <- file.path(open_ped_can_data_path, 'snv-consensus-plus-hotspots.maf.tsv.gz')
 cnv <- file.path(open_ped_can_data_path, 'consensus_wgs_plus_cnvkit_wxs.tsv.gz')

diff --git a/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.nb.html b/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.nb.html
diff --git a/analyses/gene_match/results/ensg-hugo-pmtl-mapping.tsv b/analyses/gene_match/results/ensg-hugo-pmtl-mapping.tsv
@@ -94840,4 +94840,3 @@ ENSG00000284745	AL589702.1	NA	NA
 ENSG00000284746	AC068587.10	NA	NA
 ENSG00000284747	AL034417.4	NA	NA
 ENSG00000284748	AL513220.1	NA	NA
-Symbol_Not_Found	NA	Relevant Molecular Target	PMTL version 1.1