addMetricAndArrangeGRanges {epistack} | R Documentation |
Perform an inner join between a GRanges object and a data.frame. Sort the resulting GRanges based on a metric column.
addMetricAndArrangeGRanges( gr, order, gr_key = "name", order_key = "name", order_value = "exp", shuffle_tie = TRUE )
gr |
a GRanges object. |
order |
a data.frame with at least two columns: keys and values. |
gr_key |
name of the gr metadata column containing unique names for
each genomic region in |
order_key |
name of the |
order_value |
name of the |
shuffle_tie |
a boolean Value (TRUE / FALSE). When TRUE, shuffle the GRanges before sorting, mixing the ties. |
This utility function allow the addition of a metric column to
genomic regions of interest. One of its common use case is to add
gene expression values on a set of transcription start sites.
The resulting GRanges object will only contain regions presents in both
gr
and order
.
a GRanges sorted in descending order.
data("stackepi") ramdomOrder <- data.frame(gene_id = stackepi$gene_id, value = rnorm(length(stackepi))) addMetricAndArrangeGRanges(stackepi, ramdomOrder, gr_key = "gene_id", order_key = "gene_id", order_value = "value" )