GenomicRegionsFromdataframe: Function to create a GenomiRegions object from a dataframe

Description Usage Arguments Value Author(s) See Also

Description

Function to create a GenomiRegions object from a dataframe

Usage

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GenomicRegionsFromdataframe(GenomicRegions_dataframe, ids_column=NULL, chr_column,
start_column, end_column, chromosomesNumbers=NULL,
chromosomesLabels=NULL, chromosomesLabelsInput=NULL)

Arguments

GenomicRegions_dataframe

Dataframe object containing the annotations for genomic regions

ids_column

Specify the column from the input dataframe 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 dataframe with chromosome annotations fields. Can be specified using column index (numeric) or column name (character).

start_column

Specify the column from the input dataframe 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 dataframe 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. Particularly useful when non numeric character strings are associated to each chromosome in the input file: e.g. "chr3" for chromosome "3".

Value

An object of class "GenomicRegions"

Author(s)

Francesco Ferrari

See Also

"GenomicRegions"


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