Reading in a file - Warning Message
r, read.table, warnings
Solution
you can use `readLines()` to input the data, then find the offending rows.
con <- file("path/to/file.csv", "rb")
rawContent <- readLines(con) # empty
close(con) # close the connection to the file, to keep things tidy
then take a look at `rawContent`
To find the rows with an incorrect number of columns, for example:
expectedColumns <- 2521
delim <- "\t"
indxToOffenders <-
sapply(rawContent, function(x) # for each line in rawContent
length(gregexpr(delim, x)[[1]]) != expectedColumns # count the number of delims and compare that number to expectedColumns
)
Then to read in your data:
myDataFrame <- read.csv(rawContent[-indxToOffenders], header=??, sep=delim)
Problem
I have a file that has 22268 rows BY 2521 columns. When I try to read in the file using this line of code: ``` file <- read.table(textfile, skip=2, header=TRUE, sep="\t", fill=TRUE, blank.lines.skip=FALSE) ``` But I only get 13024 rows BY 2521 columns read in and the following error: Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns I also used this command to see what rows had an incorrect number of columns: ``` x <-count.fields(textfile, sep="\t", skip=2) incorrect <- which(x != 2521) ``` and got back a list of about 20 rows that were incorrect. Is there a way to fill these rows with NA values? I thought that is what the "fill" parameter does in the read.table function, but it doesn't appear so. OR Is there a way to ignore these rows that are identified in the "incorrect" variable?