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

In alexchwong/NxtIRFcore: Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

NxtIRF Example BAMs and NxtSE Experiment Object

Description

NxtIRF_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 NxtIRFcore. See NxtIRFdata::example_bams for a description of the provided BAM files.

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

Usage

NxtIRF_example_bams()

NxtIRF_example_NxtSE()

Value

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

In NxtIRF_example_NxtSE(): returns a NxtSE object.

Functions

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

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

References

Generation of the mappability files was performed using NxtIRF 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. 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

NxtIRF_example_bams()

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

se <- NxtIRF_example_NxtSE()

alexchwong/NxtIRFcore documentation built on Oct. 31, 2022, 9:14 a.m.