SCANVIS-package {SCANVIS}R Documentation

SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

Description

SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).

Details

Package: SCANVIS
Type: Package
Title: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
Version: 1.8.0
Date: 2019-07-11
Author: Phaedra Agius <pagius@nygenome.org>
Maintainer: Phaedra Agius <pagius@nygenome.org>
Depends: R (>= 3.6)
Description: SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).
Imports: IRanges,plotrix,RCurl,rtracklayer
License: file LICENSE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews: Software,ResearchField,Transcriptomics,WorkflowStep,Annotation,Visualization
git_url: https://git.bioconductor.org/packages/SCANVIS
git_branch: RELEASE_3_14
git_last_commit: d49015e
git_last_commit_date: 2021-10-26
Date/Publication: 2021-12-14

Index of help topics:

GBM                     list of 3 TCGA glioblastoma samples, parts
                        thereof, outputs of SCANVISscan and
                        SCANVISlinkvar functions with toy variants
                        supplied for the variant-SJ mapping
IR2Mat                  IRanges to Matrix
LUAD                    list of 3 TCGA lung adenocarcinoma samples,
                        parts thereof, outputs of SCANVISscan
LUSC                    list of 3 TCGA lung squamous cell carcinoma
                        samples, parts thereof, both outputs of
                        SCANVISscan with the second sample being
                        variant-mapped via SCANVISlinkvar
SCANVIS-package         SCANVIS - a tool for SCoring, ANnotating and
                        VISualizing splice junctions
SCANVISannotation       assembles annotation from gtf file into
                        SCANVISreadable format
SCANVISexamples         Data for running SCANVISexamples
SCANVISlinkvar          maps variants to SCANVISscored junctions
SCANVISmerge            merges multiple SCANVISsamples
SCANVISread_STAR        upload SJ.tab STAR file in SCANVISuse
SCANVISscan             SCore and ANnotate splice junctions
SCANVISvisual           a sashimi-style visualization tool
gbm3                    part of a TCGA glioblastoma sample from STAR
                        alignment SJ.tab file
gbm3.vcf                a toy set of 6 variants that pair up with the
                        gbm3 data example
gen19                   parts of the annotation object created by the
                        SCANVISannotation function when used with the
                        url
                        ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/
                        which references the gencode v19 GTF file for
                        human hg19
gene2roi                gene name/s to region of interest
ls_url                  list files available at annotation/gencode url

SCANVIS is a set of tools for SCoring and ANnotating splice junctions using gencode annotation. It also has a VISualization component that allows users to quickly view one or more samples in sashimi style plots, showing splice junctions (SJs) and, optionally, a read coverage profile as well as mutations in one figure. These sashimi style plots are novel in that unannotated splice junctions are highlighted in various colours to delineate various junction types, with line styles indicating whether unannotated junctions are in frame or not.

Author(s)

Phaedra Agius <pagius@nygenome.org>

Maintainer: Phaedra Agius <pagius@nygenome.org>


[Package SCANVIS version 1.8.0 Index]