GenomicAnnotationsFromfile {PREDA} | R Documentation

## Function to create a GenomiAnnotations object from a text file

### 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)

[Package PREDA version 1.38.0 Index]