readSampleKey {HELP} | R Documentation

## Read sample key

### Description

Function to extract sample key data from a file and link chip ID information with aliases if they exist.

### Usage

    readSampleKey(file = NULL, chips = NULL, comment.char = "#", sep = "\t")

### Arguments

`file` | the name of the file containing sample key information. Each line of the file is interpreted as a single chip-to-sample map. If it does not contain an absolute path, the file name is relative to the current working directory, `getwd()`. Tilde-expansion is performed where supported. Alternatively, `file` can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). file can also be a complete URL.
`chips` | a character vector specifying a specific chip ID lookup in the sample key, for which the function will return the appropriate sample aliases
`comment.char` | character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.
`sep` | the field separator character. Values on each line of the file are separated by this character. If sep = "" the separator is "white space", that is one or more spaces, tabs, newlines or carriage returns.

### Value

Returns a character vector of sample alias information corresponding to the chips present in the sample key or a subset thereof, specified by the `chips` input.

### Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu)

### See Also

`read.table`

### Examples

    #demo(pipeline,package="HELP")

    cat("#COMMENT\nCHIP_ID\tSAMPLE\n",file="./sample.key.txt")
    write.table(cbind(1:10,1001:1010),file="./sample.key.txt",append=TRUE,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t")
    readSampleKey(file="./sample.key.txt")
    readSampleKey(file="./sample.key.txt",chips=c(7:10,"NA1","NA2"))

    #file.remove("./sample.key.txt")

[Package HELP version 1.2.0 Index]