read_factor: Read in a factor writtin in the CLS format

In ribiosIO: Input/Output Utilities of the 'ribios' Suite

Read in a factor writtin in the CLS format

Description

Read in a factor writtin in the CLS format

Usage

read_factor(con = stdin(), offset = 0)

read_cls(con = stdin(), offset = 0)

Arguments

con	File or connection to read file from
offset	The integer representing the first level, default is set to 0, for some software it can be set to 1

Value

A factor with levels as defined in the CLS file.

Note

The original CLS format specifies that both tab or space can be used as separators. This makes it unable to represent factors with sapces in levels. In order to accomodate CLS format for these factors, we propose using tab as separators in CLS files when encoding factors in R. The default setting of read_factor and write_factor uses tab. Though read_factor can handle both separators, as long as in the file a separator is consistenly used.

See Also

write_factor

Examples

set.seed(1887)
tempfac <- factor(sample(LETTERS, 30, replace=TRUE), levels=sample(LETTERS))
tempfile <- tempfile()
write_factor(tempfac, tempfile)
stopifnot(identical(tempfac, read_factor(tempfile)))

write_factor(tempfac, tempfile, sep=" ")
stopifnot(identical(tempfac, read_factor(tempfile)))

idir <- system.file("extdata", package="ribiosIO")
sample.cls <- read_factor(file.path(idir, "test.cls"))
expFac <- factor(c("Case", "Control")[c(1,0,1,0,0,1,0,0,0,1,0,1,0,0,0,1,0,1,0,0,1,1,1,1,0,0)+1],
levels=c("Case", "Control"))
stopifnot(identical(sample.cls, expFac))

ribiosIO documentation built on Feb. 20, 2026, 5:09 p.m.