GenomicRegionsFromdataframe: Function to create a GenomiRegions object from a dataframe
In PREDA: Position Related Data Analysis

Description Usage Arguments Value Author(s) See Also

View source: R/GenomicRegionsFromdataframe.R

Function to create a GenomiRegions object from a dataframe

1
2
3

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

`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".