File in out

Important libraries

connections {base}

Read in

# Read in table and fill empty values
d = read.table(fName, sep ='\t', fill = TRUE, stringsAsFactors = FALSE)

# Read in table with different seperators
d = read.delim(fName, fill = TRUE, stringsAsFactors = FALSE)
d = read.csv(fName, FALSE)

# Read json files
library(jsonlite)
a <-fromJSON(fName)

# Read excel file
library(xlsx)
wb <- loadWorkbook(file = WF_TEMPLATE_FILENAME)

# scan is more flexible but needs to know at forehand the expected data structure
d = scan(fName, what = list(character(),double(0),double()), skip =1)

# Fast read
d = fread(fName, sep ='\t', stringsAsFactors = FALSE)
# process script file
source('~/Ranalyses/PaperOneFinal/getData.R')

# Read stdout from command line pipe
readLines(pipe("ls -1")) #linux 
readLines(pipe("dir ")) #windows

cmd = "ls -1"
system(cmd, intern = T)

# Read string from file
readChar(TEMPLATE_NAME, file.info(TEMPLATE_NAME)$size)

# read large files and concatenate efficiently
listDT = list()
for (i in 1 : nrow(files)){
  f = files[i,]
  dt = fread(f$fileName)
  df$sampleId = f$sampleId  
  listDT[[i]] = dt
}
dtAll = rbindlist(listDT)

Out

# write to standard output
write.table(df, "out.txt", row.names = F, quote = F)

# write to standard output
write("My message", stdout())

# write to excel sheet
wb = createWorkbook()
sheet = createSheet(wb, sheetName = "MySheet")
addDataFrame(df, sheet, startRow = 1, startColumn = 1, row.names = FALSE)
saveWorkbook(wb, outputFile)

write(toJSON(df), stdout())

# redirect output to file
sink('data/sink.txt', append = F)
print("hello")
sink()
print("hello")

# write to standard output and quit
stop("My crash message")

#Write updating row to stdout()
cat('\rProcessed', row, 'out of',nrow(sub), 'rows. Added',nBases, 'base pairs to', newFile)
flush.console()

# quit with error status
q(status = 1)

# get files not matching a certain pattern
notOnly = !grepl('myPattern', list.files(paste0(outputFolder, '/', sampleId), pattern='withFilters')) 
list.files(paste0(outputFolder, '/', sampleId),pattern='withFilters')[notOnly]