dot-get_exons_juncs_to_plot: Obtain the details of the exons/junctions to plot

In dzhang32/RNAdiagnosR: What the Package Does (One Line, Title Case)

Description

.get_exons_juncs_to_plot plots the splicing events and coverage over a specific transcript and/or genomic region of interest. Centres around ggplot functions.

Usage

.get_exons_juncs_to_plot(gene_tx_to_plot, region_to_plot, junc_metadata,
  junc_counts_case, junc_counts_ctrl, ref)

Arguments

gene_tx_to_plot	gr. Currently only accepts an ensembl transcript id that is found in the ref input. In future, this may be extended to plot genes, however need to think about how to plot the gene_track
region_to_plot	gr. Only plot exons and juncs that overlap this region and are connected to gene_tx_to_plot
junc_metadata	gr. Junction details. Essentially must contain the co-ordinates of the junctions to plot and annotation of junctions by acceptor/donor using annotate_junc_ref
junc_counts_case	num. Vector containing the counts of cases with same order and length as junc_metadata
junc_counts_ctrl	num. Vector containing the counts of ctrls same order and length as junc_metadata
ref	gr. gtf annotation imported through rtracklayer.

dzhang32/RNAdiagnosR documentation built on Dec. 5, 2019, 2 a.m.