readRawInput: READ THE RAW DATA FILE

In ISoLDE: Integrative Statistics of alleLe Dependent Expression

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 [e-mail],
Christelle Reynès [e-mail]

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) 

ISoLDE documentation built on Jan. 10, 2021, 2:01 a.m.