readNormInput: READ THE NORMALIZED DATA FILE

In ISoLDE: Integrative Statistics of alleLe Dependent Expression

Description

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

Usage

readNormInput(norm_file, del = "\t", rownames = TRUE, colnames = 
TRUE, dec = ".")

Arguments

norm_file	A character-delimited input file containing normalized counts such as described in normASRcounts_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).
dec	Specifies the character used in the file for decimal mark (default : ".").

Value

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

Author(s)

Marine Rohmer [e-mail],
Christelle Reynès [e-mail]

See Also

normASRcounts_file.txt: the normalized ASR count file on which to run the
readNormInput function.
readRawInput: a similar function for raw (non-normalized) ASR count files.

Examples

# character-delimited input file containing normalized ASR counts
normfile <- system.file("extdata", "normASRcounts_file.txt",
package = "ISoLDE")
# loading it into a data.frame using the readNormInput function
nbreadnorm <- readNormInput(norm_file = normfile, del = "tab", 
rownames = TRUE, colnames = TRUE, dec = ".") 

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