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rdictionarypurrrseurat

using purrr::map to rename row names in elements within lists in a bigger list?


{library(Seurat)
library(tidyverse)
library(purrr)}



dirNames <- unique(dirname(list.files("data/scRNA_CITE",
                          full.names = T,
                          recursive = T)))


######


#reading multiple directories and a resultant list
dat <- purrr::map(dirNames, Read10X)
names(dat) <- dirNames

#reading just one file
#M06 <- Read10X(data.dir = "data/m06/filtered_feature_bc_matrix/")

#renaming the rows of a list element (here named antibody capture) within one list works! 
rownames(x = M06[["Antibody Capture"]]) <- gsub(pattern = "*_TotalSeqC", replacement = "", 
                                                x = rownames(x = M06[["Antibody Capture"]]))

#creating function for purrr
change_rname <- function(x){
  rownames(x[["Antibody Capture"]]) <- sub(pattern = "*_TotalSeqC", replacement = "", x[["Antibody Capture"]])
}

  
 # using the same function to rename multiple elements within multiple lists of a bigger list works temporarily BUT DOES not get saved within the bigger list
purrr::map(dat,
           ~change_rname(.x))

I am not sure how to make a reprex for this, to allow for the files to be loaded. How to make the function work with purrr and allow for within list element renaming?

Created on 2020-12-01 by the reprex package (v0.3.0)


Solution

  • Return the changed dataframe from the function.

    change_rname <- function(x){
      rownames(x[["Antibody Capture"]]) <- sub(pattern = "*_TotalSeqC",
                                           replacement = "", x[["Antibody Capture"]])
      return(x)
    }
    #apply function with `purrr:map`
    result <- purrr::map(dat,change_rname)