example-SpliceWiz-data: SpliceWiz Example BAMs and NxtSE Experiment Object

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

SpliceWiz Example BAMs and NxtSE Experiment Object

Description

SpliceWiz_example_bams() is a wrapper function to obtain and make a local copy of 6 example files provided by the NxtIRFdata companion package to demonstrate the use of SpliceWiz. See NxtIRFdata::example_bams for a description of the provided BAM files.

SpliceWiz_example_NxtSE() retrieves a ready-made functioning NxtSE object. The steps to reproduce this object is shown in the example code in makeSE

Usage

SpliceWiz_example_bams()

SpliceWiz_example_NxtSE(novelSplicing = FALSE)

Arguments

novelSplicing

Whether to import an example NxtSE with novel splice event discovery.

Value

In SpliceWiz_example_bams(): returns a 2-column data frame containing sample names and BAM paths of the example dataset.

In SpliceWiz_example_NxtSE(): returns a NxtSE object.

Functions

• SpliceWiz_example_bams(): Returns a 2-column data frame, containing sample names and sample paths (in tempdir()) of example BAM files

• SpliceWiz_example_NxtSE(): Returns a (in-memory / realized) NxtSE object that was pre-generated using the SpliceWiz example reference and example BAM files

References

Generation of the mappability files was performed using SpliceWiz using a method analogous to that described in:

Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ, Bomane A, Cosson B, Eyras E, Rasko JE, Ritchie W. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol. 2017 Mar 15;18(1):51. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13059-017-1184-4")}

See Also

makeSE

Examples

# returns a data frame with the first column as sample names, and the
# second column as BAM paths

SpliceWiz_example_bams()

# Returns a NxtSE object created by the example bams aligned to the
# mock NxtSE reference

se <- SpliceWiz_example_NxtSE()

alexchwong/SpliceWiz documentation built on March 17, 2024, 3:16 a.m.