diff --git a/analyses/gene_match/add_pmtl_ens_hugo.Rmd b/analyses/gene_match/add_pmtl_ens_hugo.Rmd
index 7b41740b04..6320dce919 100644
--- 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
index 82a9288f7f..5c778dc274 100644
--- a/analyses/gene_match/add_pmtl_ens_hugo.nb.html
+++ b/analyses/gene_match/add_pmtl_ens_hugo.nb.html
@@ -14,7 +14,7 @@
R Notebook
-
+
Load merged gene symbol + ENSG mapping file and PMTL file
library(tidyverse)── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──✔ ggplot2 3.3.5 ✔ purrr 0.3.4
-✔ tibble 3.1.5 ✔ dplyr 1.0.7
-✔ tidyr 1.1.4 ✔ stringr 1.4.0
-✔ readr 2.0.2 ✔ forcats 0.5.1✔ ggplot2 3.3.3 ✔ purrr 0.3.4
+✔ tibble 3.1.2 ✔ dplyr 1.0.6
+✔ tidyr 1.1.3 ✔ stringr 1.4.0
+✔ readr 1.4.0 ✔ forcats 0.5.1── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+
+── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()Load merged gene symbol + ENSG mapping file and PMTL file
ens_map <- read_tsv("results/ensembl_gene_symbol_gtf_genode_v28_v38_open_ped_can_v7_merged.tsv") %>%
rename(ensg_id = ensembl)Rows: 94841 Columns: 2── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
-Delimiter: "\t"
-chr (2): gene_symbol, ensembl
-ℹ Use `spec()` to retrieve the full column specification for this data.
-ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.pmtl <- read_tsv("input/PMTL_v1.1.tsv") %>%
rename(ensg_id = Ensembl_ID, pmtl = FDA_Designation)Rows: 512 Columns: 6── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
-Delimiter: "\t"
-chr (6): Ensembl_ID, Approved_Symbol, FDA_Designation, FDA_Class, FDA_Target...
-ℹ Use `spec()` to retrieve the full column specification for this data.
-ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.# add pmtl version
@@ -327,11 +321,12 @@ Are there all PMTL ensg ids included in the mapping file?
Keep the gene_symbol as in the RNA-Seq files
-
+
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")Keep the gene_symbol as in the RNA-Seq files
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
diff --git a/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.Rmd b/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.Rmd
index 4b1a8b3712..8165bece24 100644
--- 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
index 05c95b3387..f416a725f6 100644
--- a/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.nb.html
+++ b/analyses/gene_match/qc_ensg_hugo_pmtl_mapping.nb.html
@@ -14,7 +14,7 @@
QC ensg-hugo-pmtl-mapping.tsv
-
+
Load libraries
Read ensg-hugo-pmtl-mapping.tsv and OpenPedCan SNV, CNV, TPM, and fusion data
-
-open_ped_can_data_path <- '~/OpenPedCan-analysis/data/v10'
+
+open_ped_can_data_path <- '../../data/v10'
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')
@@ -247,8 +247,16 @@ Read ensg-hugo-pmtl-mapping.tsv and OpenPedCan SNV, CNV, TPM, and fusion dat
CLIN_SIG = col_character(),
PUBMED = col_character())) Warning: One or more parsing issues, see `problems()` for detailsWarning: 28 parsing failures.
+ row col expected actual file
+ 464671 AF no trailing characters 0.3618,0.0022 '../../data/v10/snv-consensus-plus-hotspots.maf.tsv.gz'
+1869464 AF no trailing characters 0.9868,0.0022 '../../data/v10/snv-consensus-plus-hotspots.maf.tsv.gz'
+1892736 AF no trailing characters 0.5821,0.1985 '../../data/v10/snv-consensus-plus-hotspots.maf.tsv.gz'
+2091025 AF no trailing characters 0.7626,0.0640 '../../data/v10/snv-consensus-plus-hotspots.maf.tsv.gz'
+4407213 AF no trailing characters 0.3618,0.0022 '../../data/v10/snv-consensus-plus-hotspots.maf.tsv.gz'
+....... ... ...................... ............. .......................................................
+See problems(...) for more details.cnv_file <- readr::read_tsv(cnv, col_types = cols())
@@ -299,7 +307,7 @@ Check gene symbol overlap
@@ -409,7 +417,7 @@ Check gene ENSG ID overlap
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
diff --git a/analyses/gene_match/results/ensg-hugo-pmtl-mapping.tsv b/analyses/gene_match/results/ensg-hugo-pmtl-mapping.tsv
index 1b871390f5..65622981e5 100644
--- 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