GenomicRegionsFromfile: Function to create a GenomiRegions object from a text file

Description Usage Arguments Value Author(s) See Also

Description

Function to create a GenomiRegions object from a text file

Usage

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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"


PREDA documentation built on May 6, 2019, 2:07 a.m.