GenomicRegionsFromfile {PREDA} | R Documentation

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

### Description

Function to create a GenomiRegions object from a text file

### Usage

    GenomicRegionsFromfile(file, ids_column=NULL, chr_column,
    start_column, end_column, chromosomesNumbers=NULL,
    chromosomesLabels=NULL, chromosomesLabelsInput=NULL, ...)

### Arguments

`file` | Path to the input txt file containing genomic regions annotations
`ids_column` | Specify the column from the input txt file with (optional) ids for genomic regions. 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. 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 region. 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 region. 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 each chromosome in the input file: e.g. "chr3" for chromosome "3".
`...` | 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 `"GenomicRegions"`

### Author(s)

Francesco Ferrari

### See Also

`"GenomicRegions"`

[Package PREDA version 1.38.0 Index]