rbind: Error in match.names(clabs, names(xi))

Question

Importing raw counts on a script in R with these necessary packages

library(optparse) 
library(DESeq2)

Then went ahead with the steps of:

obtained file names
loaded a control table
experimental table loaded
tables merged
removed extra stuff to avoid duplicates

The following error is raised when trying to import the raw counts:

Error in match.names(clabs, names(xi)) :
names do not match previous names :Calls: rbind ... eval -> eval -> eval -> rbind -> rbind -> match.names In addition: Warning message: NAs introduced by coercion

The piece of code where it fails is this:

# importing the raw counts
if (is.null(opt$raw_counts) == FALSE) {
  raw_counts_table <- read.table(counts_file, header=FALSE, sep = "\t", quote = "")
  raw_counts_table <- data.frame(raw_counts_table, 
        do.call(rbind, strsplit(as.character(raw_counts_table$V1),'_')))
  raw_counts_table$X2 <- as.numeric(as.character(raw_counts_table$X2))
  raw_counts_table <- t(raw_counts_table[,c("X2", "V2")])
  row.names(raw_counts_table) <- c("SAMPLE","RAW TOTAL")
  colnames(raw_counts_table) <- raw_counts_table[1,]
  raw_counts_table <- as.data.frame(raw_counts_table)
  raw_counts_table <- raw_counts_table[-1,]

  # Need to subtract off the total number of annotations
  raw_counts_table["ANNOTATION COUNT",] <- colSums(complete_table)
  raw_counts_table["OTHER",] <- raw_counts_table[1,] - raw_counts_table[2,]

  complete_table <- rbind(complete_table, raw_counts_table["OTHER",])
}

Seems like variable names have changed?

I had to change the actual file names (adding a prefix) on a previous step script in order to go ahead, but now as I changed the file names back to the original seems to find a mismatch between files?

I have read from other posts

Links mention the error raises when two data frames don't have the same name. How could I know where exactly is the mismatch?

Thanks!

Hi, it is great that you read other posts, but to make everyone else understand what you are dealing with, please try to make your example reproducible: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — heck1, Mar 13 '19 at 12:37
What are the colnames of `complete_table`. It would be nice if in general you could give some idea of the data you are working with. Or provide a workable alternative, if the data is sensitive. But I suspect the issue is on the last line of code, and you should compare `colnames(complete_table)` with `colnames(raw_counts_table)` — Aaron Hayman, Mar 13 '19 at 13:28

rbind: Error in match.names(clabs, names(xi))

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