GenomicAnnotationsFromfile: Function to create a GenomiAnnotations object from a text...

In PREDA: Position Related Data Analysis

Description

Function to create a GenomiAnnotations object from a text file

Usage

GenomicAnnotationsFromfile(file, ids_column, chr_column,
start_column, end_column, strand_column, chromosomesNumbers =
NULL, chromosomesLabels = NULL, chromosomesLabelsInput = NULL,
MinusStrandString = "-", PlusStrandString =
"+", optionalAnnotationsColumns = NULL, ...)

Arguments

file	Path to the input txt file containing genomic annotations
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).
chr_column	Specify the column from the input txt file with chromosome annotations fields for each ids. Can be specified using column index (numeric) or column name (character).
start_column	Specify the column from the input txt file with genomic start position for each genomic element. Can be specified using column index (numeric) or column name (character).
end_column	Specify the column from the input txt file with genomic end position for each genomic element. Can be specified using column index (numeric) or column name (character).
strand_column	Specify the column from the input txt file with genomic strand mapping for each genomic element. Can be specified using column index (numeric) or column name (character).
chromosomesNumbers	Numeric vector to specify the list of numeric values to be associated to each chromosome (especially useful for chromosomes not associated to a number such as chr X or Y)
chromosomesLabels	Character vector to specify the list of character labels to be associated to each chromosome (especially useful for chromosomes not associated to a number such as chr X or Y)
chromosomesLabelsInput	Character vector to specify the list of character labels associated to each chromosome in the input file. Particularly useful when non numeric character strings are associated to eacforh chromosome in the input file: e.g. "chr3" for chromosome "3".
MinusStrandString	Character string used to identify minus strand in the input text file
PlusStrandString	Character string used to identify plus strand in the input text file
optionalAnnotationsColumns	Character vector of columns headers or numeric vector of columns indices to specify columns of the input file containing additional annotation fields
...	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

An object of class "GenomicAnnotations"

Author(s)

Francesco Ferrari

See Also

"GenomicAnnotations"

Examples

  ## Not run: 
 
data(PREDAsampledata)
 CNdataPath <- system.file("sampledata", "CopyNumber", package =
"PREDAsampledata")
CNannotationFile <- file.path(CNdataPath , "SNPAnnot100k.csv")

CNGenomicsAnnotations<-GenomicAnnotationsForPREDAFromfile(
  file=CNannotationFile,
  ids_column=1,
  chr_column="Chromosome",
  start_column=4,
  end_column=4,
  strand_column="Strand",
  chromosomesLabelsInput=1:22,
  MinusStrandString="-", PlusStrandString="+",
  optionalAnnotationsColumns=c("Cytoband", "Entrez_gene"),
  header=TRUE, sep=",", quote="\"", na.strings = c("NA", "",
  "---"))


  
## End(Not run)

PREDA documentation built on Nov. 8, 2020, 7:40 p.m.