readRawInput {ISoLDE} | R Documentation

## READ THE RAW DATA FILE

### Description

Checks and loads into a `data.frame` the input file containing raw allele specific read (ASR) counts so that it can be input into `filterT`.

### Usage

    readRawInput(raw_file, del = "\t", rownames = TRUE, colnames =
        TRUE)

### Arguments

`raw_file` | A character-delimited input file containing raw ASR counts such as described in `rawASRcounts_file`.
`del` | Specifies the delimiter for the input file, usually a semi-colon ";", a coma "," or a tabulation "\t". (default : "\t"). Note : None of your data values must contain this delimiter (be specially careful in gene names).
`rownames` | Specifies if the file contains some row names to consider. Possible values: TRUE or FALSE (default: TRUE).
`colnames` | Specifies if the file contains some column names to consider. Possible values: TRUE or FALSE (default: TRUE).

### Details

Raw ASR counts are only required for the filtering step (with the `filterT` function) in case the normalized data do not contain 0 counts anymore. If you do not want to perform the filtering step or if you still have 0 counts in your normalized file, you do not need to load raw ASR counts. (For simplicity purpose, we call '0 count' any value of zero in a count file).

### Value

A `data.frame` containing raw ASR counts from your input file.

### Author(s)

Marine Rohmer marine.rohmer@mgx.cnrs.fr,
Christelle Reynès christelle.reynes@igf.cnrs.fr

### See Also

`rawASRcounts_file.txt`: the raw ASR count file on which to run the `readRawInput` function. `readNormInput`: a similar function for normalized ASR count file.

### Examples

    # character-delimited input file containing raw ASR counts
    rawfile <- system.file("extdata", "rawASRcounts_file.txt",
    package = "ISoLDE")
    # loading it into a data.frame using the readRawInput function
    nbread <- readRawInput(raw_file = rawfile, del = "tab",
    rownames = TRUE, colnames = TRUE)

[Package ISoLDE version 1.12.0 Index]