Use convert_gene_names() function in analysis_notebooks/ESTIMATE_tumor_purity.Rmd

[envest]

There is a function in utils/convert_gene_names.R called convert_gene_names() that converts gene names from X to Y format. Use that here instead of relying on processed_data/gene_map.tsv file and left_join().

medulloblastoma-classifier/analysis_notebooks/ESTIMATE_tumor_purity.Rmd

Lines 60 to 77 in 675c60c

	# read in gene map
	# includes ENSEMBL, ENTREZID, and SYMBOL columns for gene name conversion
	gene_map_df <- readr::read_tsv(gene_map_df_filename,
	show_col_types = FALSE)
	# convert gene names
	genex_df_SYMBOL <- genex_df %>%
	tibble::rownames_to_column(var = "ENSEMBL") %>%
	dplyr::left_join(gene_map_df %>% # do not include ENTREZID here
	dplyr::select(ENSEMBL, SYMBOL),
	by = "ENSEMBL") %>%
	dplyr::filter(!duplicated(ENSEMBL),
	!duplicated(SYMBOL),
	!is.na(SYMBOL)) %>%
	dplyr::select(SYMBOL, tidyselect::everything(), -ENSEMBL)
	readr::write_tsv(x = genex_df_SYMBOL,
	file = estimate_input_filename)