From 69cc2a2b118e4c44c0cd1a2d2b8e614557c9a9c3 Mon Sep 17 00:00:00 2001 From: Zhongli Jiang Date: Sun, 1 May 2022 02:46:32 -0400 Subject: [PATCH] add info about ensmbl id --- script/adj/protein_coding_gtex.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/script/adj/protein_coding_gtex.R b/script/adj/protein_coding_gtex.R index 99a50a2..8f0f41f 100644 --- a/script/adj/protein_coding_gtex.R +++ b/script/adj/protein_coding_gtex.R @@ -18,14 +18,14 @@ gtf_cut <- gtf[which(gtf$gene_id %in% as.matrix(POS[, 4])), ] idx_pc <- (gtf_cut[ ,12]=="protein_coding")&(gtf_cut[ ,7]=="gene") #ensembl id -#POS <- unique(gtf_cut[idx_pc, c(10, 1, 2, 3)]) +POS_ensmbl <- unique(gtf_cut[idx_pc, c(10, 1, 2, 3)]) #gene name POS <- unique(gtf_cut[idx_pc, c(13, 1, 2, 3)]) -names(POS) <- c("gene","chr","start","end") +names(POS) <- names(POS_ensmbl) <- c("gene","chr","start","end") ##16762 protein coding genes -data <- data[, match(as.matrix(POS[, 1]), as.matrix(gexp1[, 4]))] -data_rmpc <- data_rmpc[, match(as.matrix(POS[, 1]), as.matrix(gexp1[, 4]))] +data <- data[, match(as.matrix(POS_ensmbl[, 1]), as.matrix(gexp1[, 4]))] +data_rmpc <- data_rmpc[, match(as.matrix(POS_ensmbl[, 1]), as.matrix(gexp1[, 4]))] # remove genes whose size is greater than 2.3Mb distance=POS$end-POS$start