Package index

Splicejam core functions

These functions are the heart of the splicejam package

launchSashimiApp()

Launch Sashimi R-shiny application

sashimiDataConstants()

Prepare sashimi plot required data

splicejamDataFromTxDb()

Prepare splicejam data environment from a TxDb annotation package

splicejamFigure()

Make Splicejam Sashimi Figure

Detected transcripts

Method to define detected transcripts, and review results

defineDetectedTx()

Define detected transcripts

detectedTxInfo()

Summarize detected transcript results

Data import functions

Useful wrapper functions to import genomic data

getGRcoverageFromBw()

Get coverage for GRanges from bigWig files

import_juncs_from_bed()

Import splice junction data from BED or SJ.out.tab file

psl2df()

Convert PSL alignment to data.frame

Splicejam Test data

Various data objects to test Splicejam

sjenvtest

Splicejam Environment Test Data

test_cov_gr

Sample exon coverage data GRanges

test_cov_wide_gr

Sample exon coverage data GRanges with wide introns

test_exon_gr

Sample exon data GRanges

test_exon_wide_gr

Sample exon data GRanges with wide introns

test_junc_gr

Sample junction data GRangesList

test_junc_wide_gr

Sample junction data GRangesList with wide introns

Plot utility functions

Several functions, including 3-D BGA plotly function

bgaPlotly3d()

Create an interactive 3-D BGA plotly visualization

jitter_norm()

Apply jitter using normal distribution

spline3d()

Calculate a spline curve fit in 3-D

Design functions

Support for statistical design and differential isoform analysis

curateDFtoDF()

Curate data.frame into a data.frame

curateVtoDF()

Curate vector into a data.frame

groups2contrasts()

Define experimental contrasts from sample groups

runDiffSplice()

Perform differential isoform analysis using diffSplice

sortSamples()

Sort biological sample labels for experimental design

GenomicRanges functions

GenomicRanges utilities, such as annotating one GR or GRL from another

addGRgaps()

Add gaps between GRanges regions

addGRLgaps()

Add gaps between GRangesList regions

annotateGRfromGR()

Annotate GRanges using another GRanges object

annotateGRLfromGRL()

Annotate GRangesList from GRangesList objects

assignGRLexonNames()

Assign exon names to GRangesList

closestExonToJunctions()

Find closest exon to splice junction ends

findOverlapsGRL()

Find overlaps between two GRangesList objects

flattenExonsBy()

Flatten exons by gene or transcript

getGRgaps()

Get gaps in GRanges

getGRLgaps()

Get gaps in GRangesList objects

jam_isDisjoint()

Test whether GRanges are disjoint (non-overlapping)

sortGRL()

Sort GRangesList elements by chromosome and position

spliceGR2junctionDF()

Splice junction data.frame summary

GTF functions

Gene-exon structure (GTF) file parsing to tx2gene data.frame, and others.

describeGtfAttrNames()

describe gtf/gff3 attribute names by feature type

getGtfAttrs()

Grab GTF or GFF3 attributes into a data.frame

makeTx2geneFromGtf()

Make tx2gene data.frame from a GTF file

makeTx2geneFromTxdb()

Make tx2gene data.frame from a TxDb object

readGtf()

read gtf/gff3 file

ALE and codon functions

Functions supporting Farris et al, alternate last exon (ALE) and codon usage analysis.

ale2violin()

Prepare ALE data for violin plots

codonUsage2df()

Make codon usage data.frame

dna2codon()

Convert DNA to 3-base codons

getFirstStrandedFromGRL()

Get first stranded GRanges feature per GRangesList

jamCai()

Calculate Codon Adaptation Index

tx2ale()

tx2ale: detect alternative last exons (ALE) from transcript data

Shiny prep functions

Functions to prepare the Splicejam R-shiny app

sashimiAppConstants()

Sashimi Shiny app constants

sashimiAppServer()

Sashimi Shiny app server

sashimiAppUI()

Sashimi Shiny app UI

Sashimi prep functions

Functions to prepare the Sashimi data and plot objects

exoncov2polygon()

Convert exon coverage to polygons

gene2gg()

Gene GRangesList to ggplot2 grob

grl2df()

GRangesList to data.frame for ggplot2

make_ref2compressed()

Create a ref2compressed function to compress GR gaps

plotSashimi()

Jam Sashimi plot

prepareSashimi()

Prepare Sashimi plot data

ggplot2 customizations

Customizations to ggplot2 objects for Sashimi visualizations

stat_diagonal_wide_arc() geom_diagonal_wide_arc()

Draw an area defined by an upper and lower diagonal into an arc

splicejam-extensions StatDiagonalWideArc

splicejam extensions to ggforce

stat_unpack_polygon()

Stat for unpacking list-column polygon coordinates

to_basic(<GeomShape>)

Support plotly for GeomShape

Internal utility functions

Numerous utility functions, mostly for internal use within Splicejam

combineGRcoverage()

Combine GRanges coverage replicates

compressPolygonM()

Compress genome coordinates of a matrix of polygons

df2colorSub()

Convert data.frame to categorical colors

dfWide2segments()

Convert data.frame to plotly line segment format

escapeWhitespaceRegexp()

Escape whitespace in regular expression patterns

factor2label()

Convert factor to a factor label

geomean()

Classical geometric mean

intercalate()

Intercalate list values into a vector

internal_junc_score()

maximum overlapping internal junction score

jamGeomean()

Modified geometric mean for positive and negative values

list2im()

Convert list to incidence matrix

shrinkMatrix()

Shrink numeric matrix by groups of rows

simplifyXY()

Simplify XY coordinates to minimal line segments

stackJunctions()

Stack the y-axis position of junctions

strsplitOrdered()

Split the elements of an ordered factor vector