Combining duplicate genes (rows)

First we’ll load the data. Here I’m loading from an .rds file, but this could also be from a .tsv or similar file.

full_gene_matrix <- readRDS("~/Documents/projects/rgunaratna/removing_duplicate_genes/expdf_subset_ramesh.rds")
full_gene_matrix

Next, we’ll use the dplyr package to help us perform the grouping operation. You may need to install it first with install.packages("dplyr") or possibly install.packages("tidyverse").

library(dplyr)
mean_gene_matrix <- full_gene_matrix %>% group_by(gene_symbol) %>% summarise_all(funs(mean))
mean_gene_matrix

We can perform various opertaions, including median.

median_gene_matrix <- full_gene_matrix %>% group_by(gene_symbol) %>% summarise_all(funs(median))
median_gene_matrix

The results are no longer integers, which can cause issues with downstream analysis that is expecting integer counts. One can convert the values to integers by rounding. Note: You could also use the floor or ceiling functions in place of the round function, depending on your desired results.

mean_gene_matrix_rounded <- mean_gene_matrix %>% mutate_if(is.numeric, round)
mean_gene_matrix_rounded