Easy, optimized, and accurate alternative splicing analysis in R

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Documentation for package ‘SpliceWiz’ version 1.0.4

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A B C D E F G I J M N P R S T U V misc

SpliceWiz-package SpliceWiz: efficient and precise alternative splicing analysis in R

-- A --

applyFilters Filtering for IR and Alternative Splicing Events
ASE-methods Differential Alternative Splicing Event analysis
ASEFilter SpliceWiz filters to remove low-confidence alternative splicing and intron retention events
ASEFilter-class SpliceWiz filters to remove low-confidence alternative splicing and intron retention events
ASE_DESeq Differential Alternative Splicing Event analysis
ASE_DoubleExpSeq Differential Alternative Splicing Event analysis
ASE_limma Differential Alternative Splicing Event analysis
ASE_satuRn Differential Alternative Splicing Event analysis
as_ggplot_cov RNA-seq Coverage Plots and Genome Tracks

-- B --

BAM2COV Runs the OpenMP/C++ based SpliceWiz algorithm
Build-Reference-methods Builds reference files used by SpliceWiz
buildFullRef Builds reference files used by SpliceWiz
buildRef Builds reference files used by SpliceWiz

-- C --

calculateMappability Calculate low mappability genomic regions
cbind-method The NxtSE class
coerce-method The NxtSE class
collateData Collates a dataset from (processBAM) output files of individual samples
coord2GR Converts genomic coordinates into a GRanges object
Coverage Calls SpliceWiz's C++ function to retrieve coverage from a COV file
covfile The NxtSE class
covfile-method The NxtSE class
covfile<- The NxtSE class
covfile<--method The NxtSE class

-- D --

down_exc The NxtSE class
down_exc-method The NxtSE class
down_exc<- The NxtSE class
down_exc<--method The NxtSE class
down_inc The NxtSE class
down_inc-method The NxtSE class
down_inc<- The NxtSE class
down_inc<--method The NxtSE class

-- E --

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

-- F --

findBAMS Convenience Function to (recursively) find all files in a folder.
findFASTQ Convenience Function to (recursively) find all files in a folder.
findSamples Convenience Function to (recursively) find all files in a folder.
findSpliceWizOutput Convenience Function to (recursively) find all files in a folder.

-- G --

generateSyntheticReads Calculate low mappability genomic regions
getCoverage Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverageBins Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverageRegions Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverage_DF Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getDefaultFilters Filtering for IR and Alternative Splicing Events
getNonPolyARef Builds reference files used by SpliceWiz
getResources Builds reference files used by SpliceWiz
Graphics-User-Interface Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard
GUI Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard

-- I --

isCOV Validates the given file as a valid COV file

-- J --

junc_counts The NxtSE class
junc_counts-method The NxtSE class
junc_gr The NxtSE class
junc_gr-method The NxtSE class
junc_PSI The NxtSE class
junc_PSI-method The NxtSE class

-- M --

makeMatrix Construct data of percent-spliced-in (PSI) matrices and group-average PSIs
makeMeanPSI Construct data of percent-spliced-in (PSI) matrices and group-average PSIs
makeSE Imports a collated dataset into the R session as an NxtSE object
make_plot_data Construct data of percent-spliced-in (PSI) matrices and group-average PSIs
Mappability-methods Calculate low mappability genomic regions

-- N --

NxtSE The NxtSE class
NxtSE-class The NxtSE class
NxtSE-methods The NxtSE class

-- P --

plotCoverage RNA-seq Coverage Plots and Genome Tracks
plotGenome RNA-seq Coverage Plots and Genome Tracks
processBAM Runs the OpenMP/C++ based SpliceWiz algorithm

-- R --

rbind-method The NxtSE class
realize_NxtSE The NxtSE class
realize_NxtSE-method The NxtSE class
ref The NxtSE class
ref-method The NxtSE class
runFilter Filtering for IR and Alternative Splicing Events
Run_SpliceWiz_Filters Filtering for IR and Alternative Splicing Events

-- S --

sampleQC The NxtSE class
sampleQC-method The NxtSE class
sampleQC<- The NxtSE class
sampleQC<--method The NxtSE class
setSWthreads Sets the number of threads used by SpliceWiz
spliceWiz Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard
SpliceWiz_example_bams SpliceWiz Example BAMs and NxtSE Experiment Object
SpliceWiz_example_NxtSE SpliceWiz Example BAMs and NxtSE Experiment Object
STAR-methods STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_alignExperiment STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_alignReads STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_buildRef STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_mappability STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_version STAR wrappers for building reference for STAR, and aligning RNA-sequencing

-- T --

theme_white ggplot2 themes
theme_white_legend ggplot2 themes
theme_white_legend_plot_track ggplot2 themes

-- U --

up_exc The NxtSE class
up_exc-method The NxtSE class
up_exc<- The NxtSE class
up_exc<--method The NxtSE class
up_inc The NxtSE class
up_inc-method The NxtSE class
up_inc<- The NxtSE class
up_inc<--method The NxtSE class

-- V --

View-Reference-methods View SpliceWiz Reference in read-able data frames
viewASE View SpliceWiz Reference in read-able data frames
viewExons View SpliceWiz Reference in read-able data frames
viewGenes View SpliceWiz Reference in read-able data frames
viewIntrons View SpliceWiz Reference in read-able data frames
viewIR View SpliceWiz Reference in read-able data frames
viewIR_NMD View SpliceWiz Reference in read-able data frames
viewProteins View SpliceWiz Reference in read-able data frames
viewTranscripts View SpliceWiz Reference in read-able data frames

-- misc --

[-method The NxtSE class
[<--method The NxtSE class