Builds a custom table from specified user variants
build_custom_table( musica, variant_annotation, name, description = character(), data_factor = NA, annotation_df = NULL, features = NULL, type = NULL, color_variable = NULL, color_mapping = NULL, return_instead = FALSE, overwrite = FALSE )
musica | A |
---|---|
variant_annotation | User column to use for building table |
name | Table name to refer to (must be unique) |
description | Optional description of the table content |
data_factor | Full set of table values, in case some are missing from the data. If NA, a superset of all available unique data values will be used |
annotation_df | A data.frame of annotations to use for plotting |
features | A data.frame of the input data from which the count table will be built |
type | The type of data/mutation in each feature as an Rle object |
color_variable | The name of the column of annotation_df used for the coloring in plots |
color_mapping | The mapping from the values in the selected color_variable column to color values for plotting |
return_instead | Instead of adding to musica object, return the created table |
overwrite | Overwrite existing count table |
If return_instead = TRUE then the created table object is returned, otherwise the table object is automatically added to the musica's count_tables list and nothing is returned
data(musica) annotate_transcript_strand(musica, "19", build_table = FALSE) #> 403 genes were dropped because they have exons located on both strands #> of the same reference sequence or on more than one reference sequence, #> so cannot be represented by a single genomic range. #> Use 'single.strand.genes.only=FALSE' to get all the genes in a #> GRangesList object, or use suppressMessages() to suppress this message. build_custom_table(musica, "Transcript_Strand", "Transcript_Strand", data_factor = factor(c("T", "U")))