View source: R/exon_in_intron.R
exon_in_intron | R Documentation |
Annotate if there is an exon within an intron
exon_in_intron(df, transcripts)
df |
A data.frame with splice junctions in rows and at least the columns:
|
transcripts |
a GRangesList with transcripts defined as GRanges of exons
created by |
A data.frame as the input but with potentially multiple rows
and with the additional column(s):
- exon_free
: Boolean indicating if the given IR junctions is exon-free. Will return NA for non-intron retentions.
library(dplyr)
toy_tx <- GenomicRanges::GRangesList(list(
tx1 = GenomicRanges::GRanges(
c("1", "1", "1"),
IRanges::IRanges(
c(2, 15, 27),
c(8, 23, 35),
),
strand = c("+", "+", "+")
),
tx1a = GenomicRanges::GRanges(
c("1" ),
IRanges::IRanges(
c(3),
c(10),
),
strand = c("+")
)))
df <- tibble(
junc_id = c("1:8-9:+", "1:14-15:+"),
tx_id = c("tx1", "tx1")
)
df1 <- df %>%
exon_in_intron(transcripts = toy_tx)
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