ISoLDE (version 1.0.2)

readRawInput: 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).

Value

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

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).

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)