cough cough couhg

R/get_protein_encoding.R

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+library(tidyverse)
+library(biomaRt)
+###get protein encoding only genes from expression matrices
+
+ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")                                                                         
+filters = listFilters(ensembl)                                                                                                        
+myResult <- getBM(attributes = c("ensembl_gene_id", "gene_biotype", "hgnc_symbol"), mart=ensembl)
+protein_coding <- filter(myResult, gene_biotype == "protein_coding")
+protein_coding_list <- protein_coding$hgnc_symbol
+#where cl_cpm_fil_t_cor is a matrix with col and row names of the gene symbols
+all_hek293t_subset <- cl_cpm_fil_t_cor[rownames(cl_cpm_fil_t_cor)%in%protein_coding_list,colnames(cl_cpm_fil_t_cor)%in%protein_coding_list]
+
+cl_cpm_fil_t_cor_small_hek293t <- all_hek293t_subset[1:100, 1:100]
+write.table(all_hek293t_subset, "../output/all_hek293t_subset.csv", sep = ",", quote = F)
+
+#for input k562
+k562 <- read.table("../data/perturb_rbp_coexp.csv/perturb_rbp_coexp.csv", sep = ",", header = T)
+k562_genes <- colnames(k562)
+k562$genes <- k562_genes
+rownames(k562) <- k562[,17893]
+
+all_k562_subset <- k562[rownames(k562)%in%protein_coding_list,colnames(k562)%in%protein_coding_list]
+
+all_k562_subset_small <- all_k562_subset[1:10, 1:10]
+write.table(all_k562_subset, "../output/all_k562_subset.csv", sep = ",", quote = F)