From f5b4e45741bb538a9d60f73a35349abf59102954 Mon Sep 17 00:00:00 2001 From: Obi Griffith Date: Wed, 19 Jun 2024 12:16:14 -0400 Subject: [PATCH] drop some legacy code --- _posts/0003-04-01-DE_Visualization_Ballgown.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/_posts/0003-04-01-DE_Visualization_Ballgown.md b/_posts/0003-04-01-DE_Visualization_Ballgown.md index 94a3b94..3e45c99 100644 --- a/_posts/0003-04-01-DE_Visualization_Ballgown.md +++ b/_posts/0003-04-01-DE_Visualization_Ballgown.md @@ -69,7 +69,6 @@ transcript_expression = as.data.frame(texpr(bg)) #View expression values for the transcripts of a particular gene symbol of chromosome 22. e.g. 'TST' #First determine the transcript_ids in the data.frame that match 'TST', aka. ENSG00000128311, then display only those rows of the data.frame -#i=bg_table[,"gene_id"]=="ENSG00000128311" i=bg_table[,"gene_name"]=="TST" bg_table[i,] @@ -81,8 +80,6 @@ ballgown::geneNames(bg)[2763] #What if we want to view values for a list of genes of interest all at once? genes_of_interest = c("TST", "MMP11", "LGALS2", "ISX") -#genes_of_interest = c("ENSG00000128311","ENSG00000099953","ENSG00000100079","ENSG00000175329") -#i = bg_table[,"gene_id"] %in% genes_of_interest i = bg_table[,"gene_name"] %in% genes_of_interest bg_table[i,]