get_event_annotations: Annotate event names to event length, seq and GC.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Annotate event names to event length, seq and GC.

Description

Annotate event names to event length, seq and GC.

Usage

get_event_annotations(se, event_names, org = "hs", prefix = "")

Arguments

se	an object of class NxtSE.
event_names	a character vector denoting valid event names.
org	a character string "hs" or "mm".
prefix	a character string, usually "chr", to append in the chromosome names. This is useful when event names are without "chr" prefix while BSgenome contains "chr".

Value

GenomicRanges.

Examples

se <- SpliceWiz::SpliceWiz_example_NxtSE(novelSplicing = TRUE)
SpliceWiz::colData(se)$treatment <- rep(c("A", "B"), each = 3)
SpliceWiz::colData(se)$replicate <- rep(c("P","Q","R"), 2)
res <- run_ase_diff_analysis(x = se, test_factor = "treatment", test_nom = "A" ,test_denom = "B",  IRmode ="annotated",  cutoff_lfc = 0.6, cutoff_pval = 1, regul_based_upon = 1)
q_events <- get_ASE_by_regulation(res, sample_comparisons = "A_VS_B",regulation = "both") %>% names()
get_event_annotations(se = se, event_names = q_events)

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.