Create objects of class AnnotationTrack

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Description

Convenience function for constructing objects of class AnnotationTrack.

Usage

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makeAnnotationTrack(regions = NULL, chr = NULL, strand = NULL, start = NULL, end = NULL, feature = NULL, group = NULL, ID = NULL, dp = NULL)

Arguments

regions

A dataframe with columns start, end, feature, group, ID. start and end delineate the boundaries of the boxes feature can be used to color the boxes. Group denotes linking so generally exons from a gene form a group. Finally, ID can be used to plot names on boxes.

chr

The chromosome of the regions (can be ignored)

strand

The strand of the regions (can be ingored)

start

If regions is missing then we construct a dataframe from the remaining parameters.

end

Construct regions with this vector

feature

Construct regions with this feature vector or scalar

group

Defines a grouping

ID

Defines an ID for each annotation bit

dp

DisplayPars, in this case we can create a mapping between feature and color. So lets say in the feature column you have: gene, transcript, gene, then in the dp you can say gene = 'blue' and transcript = 'green'

Value

Returns an object of class AnnotationTrack

Examples

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a <-  makeAnnotationTrack(start = c(10, 15, 25), end = c(12, 19, 31),
                      group = c(1,1,2), feature = c("gene", "gene", "tf"),
                      ID = paste("id", 1:3, sep = ""), dp = DisplayPars(gene = 'blue'))
gdPlot(a, minBase = 0, maxBase = 40)

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