I would like to read multiple text files from my directory the files are arranged in following format
regional_vol_GM_atlas1.txt
regional_vol_GM_atlas2.txt
........
regional_vol_GM_atlas152.txt
Data from the files looks in following format
667869 667869
580083 580083
316133 316133
3631 3631
following is the script that i have written
library(readr)
library(stringr)
library(data.table)
array <- c()
for (file in dir(/media/dev/Daten/Task1/subject1/t1)) # path to the directory where .txt files are located
{
row4 <- read.table(file=list.files(pattern ="regional_vol*.txt"),
header = FALSE,
row.names = NULL,
skip = 3, # Skip the 1st 3 rows
nrows = 1, # Read only the next row after skipping the 1st 3 rows
sep = "\t") # change the separator if it is not "\t"
array <- cbind(array, row4)
}
I am incurring following error
Error in file(file, "rt") : invalid 'description' argument
kindly suggest me where i was wrong in the script
This seems to work fine for me. Make changes as per code comments in case files have headers : [Answer Edited to reflect new information posted by OP]
# rm(list=ls()) #clean memory if you can afford to
mydir<- "~/Desktop/a" #change as per your path
# read full paths
myfiles<- list.files(mydir,pattern = "regional_vol*",full.names=T)
myfiles #check that files listed correctly
# initialise the dataframe from first file
# change header =T/F depending on presence of header
# make sure sep is correct
df<- read.csv( myfiles[1], header = F, skip = 0, nrows = 4, sep="" )[-c(1:3),]
#check that first line was read correctly
df
#read all the other files and update dataframe
#we read 4 lines to read the header correctly, then remove 3
ans<- lapply(myfiles[-1], function(x){ read.csv( x, header = F, skip = 0, nrows = 4, sep="")[-c(1:3),] })
ans
#update dataframe
lapply(ans, function(x){df<<-rbind(df,x)} )
#this should be the required dataframe
df
Also, if you are on Linux, a much simple method would be to simply make the OS do it for you
awk 'FNR == 4' regional_vol*.txt