StatisticsForPREDAFromfile: Function to create a StatisticsForPREDA objet from a txt file

Description

Function to create a StatisticsForPREDA objet from a txt file

Usage

StatisticsForPREDAFromfile(file, ids_column = NULL,
statistic_columns = NULL, analysesNames = NULL, testedTail =
c("upper", "lower", "both"), ...)

Arguments

file

Path to the input txt file containing statistics on genomics data

ids_column

Specify the column from the input txt file with gene (or other genomic features) ids. Can be specified using column index (numeric) or column name (character).

statistic_columns

Specify the column (or columns) from the input txt file with gsta.enomic data statistics that will be included in the statisticsForPREDA object. Can be specified using column index (numeric) or column name (character).

If NULL (default), all columns excluding ids_column will be considered as input statistics

analysesNames

Names (labels) to be associated to each input statistic. If NULL the column names for statistics_columns will be used.

testedTail

Specify what tail of the distribution will be tested for significantly extreme values in PREDA analysis. Possible values are "both", "upper" or "lower".

...

any other parameter for read.table function that could be useful for parsing the input file, such as "sep", "quote", "header", "na.strings" and other parameters.

Value

A statisticsForPREDA object

Details

A txt file is parsed and a statisticsForPREDA object is built using contained data.

Examples

Run this code

  ## Not run: 
# require(PREDAsampledata)
# 
# CNdataPath <- system.file("sampledata", "CopyNumber", package =
# "PREDAsampledata")
# 
# CNdataFile <- file.path(CNdataPath , "CNAG_data_PREDA.txt")
# 
# CNannotationFile <- file.path(CNdataPath , "SNPAnnot100k.csv")
# 
# CNStatisticsForPREDA<-StatisticsForPREDAFromfile(file=CNdataFile,
# ids_column="AffymetrixSNPsID", testedTail="both", sep="\t",
# header=TRUE)
# 
#   ## End(Not run)