ASpli-package {ASpli} | R Documentation

## Analysis of alternative splicing using RNAseq

### Description

ASpli is an integrative and flexible package that facilitates the characterization of genome-wide changes in AS under different experimental conditions. ASpli analyzes the differential usage of introns, exons, and splice junctions using read counts, and estimates the magnitude of changes in AS by calculating differences in the percentage of exon inclusion or intron retention using splice junctions. This integrative approach allows the identification of changes in both annotated and novel AS events.

ASpli allows users to produce self-explanatory intermediate outputs, based on the aim of their analysis. A typical workflow involves parsing the genome annotation into new features called bins, overlapping read alignments against those bins, and inferring differential bin usage based on the number of reads aligning to the bins and junctions.

### Details

Package: | ASpli
Type: | Package
Version: | 1.5.1
Date: | 2018-02-22
License: | GPL
Depends: | methods, GenomicRanges, GenomicFeatures, edgeR, methods, BiocGenerics, IRanges, GenomicAlignments, Gviz

### Author(s)

Estefania Mancini, Javier Iserte, Marcelo Yanovsky and Ariel Chernomoretz

### References

- Acute effects of light on alternative splicing in light-grown plants. Photochemistry and Photobiology. Mancini, E, Sanchez, S, Romanowsky, A, Yanovsky, MJ. DOI: 10.1111/php.12550

- GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms in Arabidopsis thaliana. Proceedings of the National Academy of Sciences. Schlaen, RG, Mancini, E, Sanchez, SE, Perez-Santangelo, S, Rugnone, ML, Simpson, CG, Brown, JWS, Zhang, X, Chernomoretz, A, Yanovsky, MJ. DOI:10.1073/pnas.1504541112

- Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome. BMC Genomics. Hernando, E, Sanchez, S, Mancini, E, Yanovsky MJ. DOI:10.1186/s12864-015-1399-2

- A role for LSM genes in the regulation of circadian rhythms. Proceedings of the National Academy of Sciences. Perez Santangelo, S, Mancini, E, Francey, LJ, Schlaen, RG, Chernomoretz, A, Hogenesch, JB, Yanovsky MJ. DOI: 10.1073/pnas.1409791111

- The dengue virus NS5 protein intrudes in the cellular spliceosome and modulates splicing. PLOS Pathogens. De Maio, F., Risso, G., Iglesias, G., Shah, P, Pozzi, B., Gebhard, L., Mammi, L., Mancini, E., Yanovsky, M., Andino, R., Krogan, N., Srebrow, A. and Gamarnik, A. DOI:10.1371/journal.ppat.1005841

### Examples

      # Create a transcript DB from gff/gtf annotation file.
      # Warnings in this examples can be ignored.
      library(GenomicFeatures)
      genomeTxDb <- makeTxDbFromGFF( system.file('extdata','genes.mini.gtf',
                                     package="ASpli") )

      # Create an ASpliFeatures object from TxDb
      features <- binGenome( genomeTxDb )

      # Define bam files, sample names and experimental factors for targets.
      bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam",
                         "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )
      targets <- data.frame(
                   row.names = paste0('Sample_',c(1:6)),
                   bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
                   factor1 = c( 'C','C','C','D','D','D') )

      # Load reads from bam files
      bams <- loadBAM( targets )

      # Read counts from bam files
      counts   <- readCounts( features, bams, targets, cores = 1, readLength = 100,
                              maxISize = 50000 )

      # Calculate differential usage of genes, bins and junctions
      du       <- DUreport( counts, targets )
      du       <- junctionDUreport( counts, targets, appendTo = du)

      # Calculate PSI / PIR for bins and junction.
      as       <- AsDiscover( counts, targets, features, bams, readLength = 100,
                              threshold = 5, cores = 1 )

[Package ASpli version 1.12.0 Index]