Usage
GenomicAnnotationsFromdataframe(GenomicAnnotations_dataframe, ids_column, chr_column,
start_column, end_column, strand_column, chromosomesNumbers =
NULL, chromosomesLabels = NULL, chromosomesLabelsInput = NULL,
MinusStrandString = "-", PlusStrandString =
"+", optionalAnnotationsColumns = NULL)
Arguments
GenomicAnnotations_dataframe
Dataframe object contanining 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