profile scores

profiles.R

# Suppose you have some files that look like this:
# bmi_chr01.profile
# bmi_chr02.profile
# bmi_chr03.profile
# etc

# Read in each profile score
l <- list()
j <- 1
for(i in 1:22)
{
	# Add leading zeros to i
	ii <- sprintf("%02d", i)
	profile_file <- paste0("bmi_chr", ii, ".profile")
	if(file.exists(profile_file))
	{
		message("reading ", profile_file)
		l[[j]] <- read.table(profile_file, header=TRUE)
		j <- j + 1
	}
}

# Now we have a list with 22 different data frames
# Need to extract the "SCORESUM" columns from each data frame

scores_chr <- sapply(l, function(x) { 
	a <- x$SCORESUM
})

# Now we have a matrix of the scores for each chromosome
# To get a single score we just sum each row

scores <- rowSums(scores_chr)