Package 'SPLINTER' reference manual

Title:	Splice Interpreter of Transcripts
Description:	Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.
Authors:	Diana Low [aut, cre]
Maintainer:	Diana Low <[email protected]>
License:	GPL-2
Version:	1.31.0
Built:	2024-09-11 05:56:53 UTC
Source:	https://github.com/bioc/SPLINTER

acceptor.m

Description

Acceptor site mammalian frequency matrices for GT-AG pairs from SpliceDB

Usage

data("acceptor.m")data("acceptor.m")

Format

The format is: num [1:4, 1:15] 9 31.03 12.5 42.36 8.44 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:4] "A" "C" "G" "T" ..$ : chr [1:15] "V1" "V2" "V3" "V4" ...

Source

http://www.softberry.com/spldb/SpliceDB.html

References

Burset M., Seledtsov I., Solovyev V. (Nucl.Acids Res.,2000,28,4364-4375; Nucl. Acids Res.,2001,29,255-259)

Examples

data(acceptor.m)
data(acceptor.m)

addEnsemblAnnotation

Description

Adds annotation to extractSpliceEvents object (if not present)

Usage

addEnsemblAnnotation(data, species = "hsapiens")
addEnsemblAnnotation(data, species = "hsapiens")

Arguments

`data`	`extractSpliceEvents` object
`species`	character. biomaRt species passed to retrieve annotation. Common species include: 'hsapiens','mmusculus'

Value

extractSpliceEvents object with annotated genes under $geneSymbol

Author(s)

Diana Low

Examples

data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
#splice_data<-addEnsemblAnnotation(data=splice_data,species="mmusculus")
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
#splice_data<-addEnsemblAnnotation(data=splice_data,species="mmusculus")

annotateEvents

Description

Gives detailed description of splicing event in terms of splicing outcome post translation. Currently supports exon skipping and intron retention events.

Usage

annotateEvents(
  thedata,
  db,
  bsgenome,
  outputdir,
  full_output = FALSE,
  output_prefix = "results"
)
annotateEvents(
  thedata,
  db,
  bsgenome,
  outputdir,
  full_output = FALSE,
  output_prefix = "results"
)

Arguments

`thedata`	list. output of extractSpliceEvents.
`db`	TxDb object
`bsgenome`	BSGenome object
`outputdir`	character. relative output directory to current location.
`full_output`	logical. writes out detailed text report and generate figures.
`output_prefix`	character. text prefix for full_output files.

Value

list containing information on (1) data.frame with splicing regions (2) splice event type

Author(s)

Diana LOW

callPrimer3

Description

call primer3 for a given set of DNAstringSet object

Usage

callPrimer3(
  seq,
  size_range = "150-500",
  Tm = c(57, 59, 62),
  name = "Primer1",
  primer3 = "primer3-2.3.7/bin/primer3_core",
  thermo.param = "primer3-2.3.7/src/primer3_config/",
  sequence_target = NULL,
  settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt"
)
callPrimer3(
  seq,
  size_range = "150-500",
  Tm = c(57, 59, 62),
  name = "Primer1",
  primer3 = "primer3-2.3.7/bin/primer3_core",
  thermo.param = "primer3-2.3.7/src/primer3_config/",
  sequence_target = NULL,
  settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt"
)

Arguments

`seq`	DNAstring object, one DNA string for the given amplicon
`size_range`	default: '151-500'
`Tm`	melting temprature parameters default:c(55,57,58)
`name`	name of the amplicon in chr_start_end format
`primer3`	primer3 path
`thermo.param`	thermodynamic parameters folder
`sequence_target`	If one or more targets is specified then a legal primer pair must flank at least one of them.
`settings`	text file for parameters

Details

modified to include SEQUENCE_TARGET as an option

Value

data.frame of designed primers and parameters

Author(s)

Altuna Akalin's modified Arnaud Krebs' original function further modified here by Diana Low

Examples

### NOT RUN ###
# primer_results<-callPrimer3(seq='')

### NOT RUN ###
# primer_results<-callPrimer3(seq='')

checkPrimer

Description

checkPrimer

Usage

checkPrimer(pp, genome, roi = NULL)
checkPrimer(pp, genome, roi = NULL)

Arguments

`pp`	data.frame defining primers, or output of `callPrimer3`. minimal columns = PRIMER_LEFT_SEQUENCE,PRIMER_RIGHT_SEQUENCE
`genome`	BSgenome object
`roi`	`makeROI` object

Value

list of GRanges with primer locations

Author(s)

Diana Low

Examples

# create a primer pair
roi
primer_pair <- data.frame(PRIMER_LEFT_SEQUENCE="agctcttgaaattggagctgac",
                          PRIMER_RIGHT_SEQUENCE="cttagaaagaacaggaaatcc",
                          stringsAsFactors=FALSE)
# create a primer pair
roi
primer_pair <- data.frame(PRIMER_LEFT_SEQUENCE="agctcttgaaattggagctgac",
                          PRIMER_RIGHT_SEQUENCE="cttagaaagaacaggaaatcc",
                          stringsAsFactors=FALSE)

compatible_cds

Description

compatible_cds

Examples

data(compatible_cds)
## maybe str(compatible_cds) ; plot(compatible_cds) ...
data(compatible_cds)
## maybe str(compatible_cds) ; plot(compatible_cds) ...

compatible_tx

Description

compatible_tx

Examples

data(compatible_tx)
## maybe str(compatible_tx) ; plot(compatible_tx) ...
data(compatible_tx)
## maybe str(compatible_tx) ; plot(compatible_tx) ...

donor.m

Description

Donor site mammalian frequency matrices for GT-AG pairs from SpliceDB

Usage

data("donor.m")data("donor.m")

Format

The format is: num [1:4, 1:9] 34.1 36.2 18.3 11.4 60.4 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:4] "A" "C" "G" "T" ..$ : chr [1:9] "V1" "V2" "V3" "V4" ...

Source

http://www.softberry.com/spldb/SpliceDB.html

References

Burset M., Seledtsov I., Solovyev V. (Nucl.Acids Res.,2000,28,4364-4375; Nucl. Acids Res.,2001,29,255-259)

Examples

data(donor.m)
data(donor.m)

eventOutcomeCompare

Description

Compares two sequences and gives differences if there's a switch from 1->2 if seq2 is NULL, assume seq1 is a list of length 2 to compare

Usage

eventOutcomeCompare(
  seq1,
  seq2 = NULL,
  genome,
  direction = TRUE,
  fullseq = TRUE,
  verbose = FALSE
)
eventOutcomeCompare(
  seq1,
  seq2 = NULL,
  genome,
  direction = TRUE,
  fullseq = TRUE,
  verbose = FALSE
)

Arguments

`seq1`	GRangesList
`seq2`	GRangesList
`genome`	BSGenome object
`direction`	logical. Report direction of sequence change.
`fullseq`	logical. Report full sequences.
`verbose`	logical. turn messages on/off.

Value

list containing
(1) tt : PairwiseAlignmentsSingleSubject pairwise alignment
(2) eventtypes : string detailing primary event classification

Author(s)

Diana LOW

Examples

suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
eventOutcomeCompare(seq1=compatible_cds$hits[[1]],seq2=region_minus_exon,
 genome=bsgenome,direction=TRUE)
suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
eventOutcomeCompare(seq1=compatible_cds$hits[[1]],seq2=region_minus_exon,
 genome=bsgenome,direction=TRUE)

eventOutcomeTranslate

Description

translates sequences, reports if NMD or NTC

Usage

eventOutcomeTranslate(
  seq1,
  genome,
  direction = FALSE,
  fullseq = TRUE,
  verbose = FALSE
)
eventOutcomeTranslate(
  seq1,
  genome,
  direction = FALSE,
  fullseq = TRUE,
  verbose = FALSE
)

Arguments

`seq1`	GRangesList
`genome`	BSGenome object
`direction`	logical. Report direction of sequence change.
`fullseq`	logical. Output full AA sequence.
`verbose`	logical. turn messages on/off.

Value

list of translated sequences

Author(s)

Diana LOW

Examples

suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
translation_results<-eventOutcomeTranslate(compatible_cds,genome=bsgenome,
 direction=TRUE)
suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
translation_results<-eventOutcomeTranslate(compatible_cds,genome=bsgenome,
 direction=TRUE)

eventPlot

Description

eventPlot

Usage

eventPlot(
  transcripts,
  roi_plot = NULL,
  bams = c(),
  names = c(),
  annoLabel = c("Gene A"),
  rspan = 1000,
  pfam_dom = NULL,
  showAll = TRUE
)
eventPlot(
  transcripts,
  roi_plot = NULL,
  bams = c(),
  names = c(),
  annoLabel = c("Gene A"),
  rspan = 1000,
  pfam_dom = NULL,
  showAll = TRUE
)

Arguments

`transcripts`	GRanges object
`roi_plot`	GRanges object region to plot
`bams`	character vector of bam file locations
`names`	character vector of name labels
`annoLabel`	character. annotation label
`rspan`	integer or NULL. number of basepairs to span from roi. if NULL, will consider whole gene of roi
`pfam_dom`	optional GRanges object of PFAM domains from UCSC Tables.
`showAll`	logical. TRUE = display splice junctions of entire view or FALSE = just roi.

Value

a Gviz plot of genomic region

Author(s)

Diana Low

Examples

# define BAM files
data_path<-system.file("extdata",package="SPLINTER")
mt<-paste(data_path,"/mt_chr14.bam",sep="")
wt<-paste(data_path,"/wt_chr14.bam",sep="")

# plot results
eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt),
 names=c('wt','mt'),rspan=1000)
# define BAM files
data_path<-system.file("extdata",package="SPLINTER")
mt<-paste(data_path,"/mt_chr14.bam",sep="")
wt<-paste(data_path,"/wt_chr14.bam",sep="")

# plot results
eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt),
 names=c('wt','mt'),rspan=1000)

extendROI

Description

extend the span of the current ROI by n number of up/downstream exon(s) by modifying roi_range within the makeROI object while retaining legacy sites by keeping $roi and $flank

Usage

extendROI(roi, tx, up = 0, down = 0, type = 1)
extendROI(roi, tx, up = 0, down = 0, type = 1)

Arguments

`roi`	`makeROI` object
`tx`	GRangesList transcript list to pull regions from
`up`	integer. number of exons to extend upstream
`down`	integer. number of exons to extend downstream
`type`	integer. 1=full cassette, 2=flank only

Value

makeROI object with modified ranges

Examples

extendROI(roi,valid_tx,up=1)
extendROI(roi,valid_tx,up=1)

extractSpliceEvents

Description

Extracts the location of target, upstream and downstream splice sites Used for calculations and genome visualizations

Usage

extractSpliceEvents(
  data = NULL,
  filetype = "mats",
  splicetype = "SE",
  fdr = 1,
  inclusion = 1,
  start0 = TRUE
)
extractSpliceEvents(
  data = NULL,
  filetype = "mats",
  splicetype = "SE",
  fdr = 1,
  inclusion = 1,
  start0 = TRUE
)

Arguments

`data`	character. path to file
`filetype`	character. type of splicing output. c('mats','custom'). see Details.
`splicetype`	character. c('SE', 'RI', 'MXE', 'A5SS', 'A3SS')
`fdr`	numeric. false discovery rate filter range [0,1]
`inclusion`	numeric. splicing inclusion range, takes absolute value
`start0`	boolean 0-base start

Details

filetype 'custom' should provide a 9-column tab-delimited text file with the following columns: ID (Ensembl gene id), Symbol (gene name), chr, strand, exonStart, exonEnd, exon2Start, exon2End, upstreamStart, upstreamEnd, downstreamStart, downstreamEnd eg. ENSG0000012345 chr1 + 3 4 5 6 1 2 7 8

Value

list containing information on
(1) original file type
(2) splice event type
(3) data.frame with splicing regions

Author(s)

Diana Low

Examples

data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))

extractSpliceSites

Description

Extracts and formats to bed the location of target, upstream and downstream splice sites

Usage

extractSpliceSites(
  df,
  target = "SE",
  site = "donor",
  motif_range = c(-3, 6),
  start0 = TRUE
)
extractSpliceSites(
  df,
  target = "SE",
  site = "donor",
  motif_range = c(-3, 6),
  start0 = TRUE
)

Arguments

`df`	extractSpliceEvents object
`target`	the target site to extract. See Details.
`site`	character donor or acceptor
`motif_range`	numeric vector of splice position to extract
`start0`	boolean 0-base start

Details

target : the site to extract the sequence from. It can be either the event in question (SE, RI, MXE - first exon, MXE2 - second exon, A5SSlong, A5SSshort, A3SSlong, A3SSshort, upstream or downstream). If this function is used in conjunction with shapiroDonor or shapiroAcceptor to compute scores, then most likely it will be run twice - once for the event, and the other either up- or downstream as a comparison.

Value

GRanges object

Author(s)

Diana Low

Examples

data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data,target="SE")
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data,target="SE")

findCompatibleEvents

Description

Which transcript contains the event? Each event has 2 possibilities, as long as the transcript fulfills one, it passes the test Has to be exact (inner junctions)

Usage

findCompatibleEvents(tx, tx2 = NULL, roi, sequential = TRUE, verbose = FALSE)
findCompatibleEvents(tx, tx2 = NULL, roi, sequential = TRUE, verbose = FALSE)

Arguments

`tx`	GRangesList object of transcripts
`tx2`	optional GRangesList object of transcripts if tx is list of cds
`roi`	`makeROI` object contaning event information
`sequential`	logical. Exons have to appear sequentially to be considered compatible
`verbose`	logical. printouts and messages.

Details

Seperates into event/region1 and 2 for the alternative case

Value

list of length 4
(1) GRangesList
(2) Hits status [c]=coding; [nc]=non-coding
(3) ct - compatible transcripts
(4) tt - total transcripts

Author(s)

Diana Low

Examples

compatible_cds <- findCompatibleEvents(valid_cds,roi=roi,verbose=TRUE)
compatible_cds <- findCompatibleEvents(valid_cds,roi=roi,verbose=TRUE)

findCompatibleExon

Description

Finds compatible exon in annotation with the one present in roi object

Usage

findCompatibleExon(tx, roi, verbose = FALSE)
findCompatibleExon(tx, roi, verbose = FALSE)

Arguments

`tx`	GRangesList object of transcripts
`roi`	`makeROI` object contaning event information
`verbose`	logical. printouts and messages.

Value

list of length 3
(1) GRangesList hits
(2) Number of transcripts
(3) Original number of input transcripts

Author(s)

Diana Low

Examples

compatible_exons <- findCompatibleExon(valid_cds,roi)
compatible_exons <- findCompatibleExon(valid_cds,roi)

findTX

Description

Given an ENSEMBL id, find all transcripts that matches id

Usage

findTX(id, db, tx, valid = FALSE, verbose = FALSE)
findTX(id, db, tx, valid = FALSE, verbose = FALSE)

Arguments

`id`	character. transcript identification (currently ENSEMBL gene names)
`db`	TxDb object
`tx`	GRangesList
`valid`	logical. check if in multiples of 3 [TRUE] for CDS translation.
`verbose`	logical. turn messages on/off.

Value

GRangesList

Author(s)

Diana Low

Examples

valid_cds <-findTX(id=splice_data$data[2,]$ID,tx=thecds,db=txdb,valid=FALSE)
valid_cds <-findTX(id=splice_data$data[2,]$ID,tx=thecds,db=txdb,valid=FALSE)

getPCRsizes

Description

returns length of product given a GRanges span and GRangesList of transcripts

Usage

getPCRsizes(pcr_span, txlist, verbose = FALSE)
getPCRsizes(pcr_span, txlist, verbose = FALSE)

Arguments

`pcr_span`	GRanges object
`txlist`	GRangesList object
`verbose`	logical. report intermediate output.

Value

data.frame of transcript names with detected sizes in basepairs

Author(s)

Diana Low

Examples

suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
## create a primer pair
## for actual use, obtain primer pair from primer design (callPrimer3)
primer_pair <- data.frame(PRIMER_LEFT_SEQUENCE="agctcttgaaattggagctgac",
                          PRIMER_RIGHT_SEQUENCE="cttagaaagaacaggaaatcc",
                          stringsAsFactors=FALSE)

## confirm location
cp<-checkPrimer(primer_pair,bsgenome,roi)
cp

## get the PCR sizes
pcr_result1 <- getPCRsizes(cp,theexons)
suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
## create a primer pair
## for actual use, obtain primer pair from primer design (callPrimer3)
primer_pair <- data.frame(PRIMER_LEFT_SEQUENCE="agctcttgaaattggagctgac",
                          PRIMER_RIGHT_SEQUENCE="cttagaaagaacaggaaatcc",
                          stringsAsFactors=FALSE)

## confirm location
cp<-checkPrimer(primer_pair,bsgenome,roi)
cp

## get the PCR sizes
pcr_result1 <- getPCRsizes(cp,theexons)

getRegionDNA

Description

get DNA sequence give a region of interest

Usage

getRegionDNA(roi, genome, introns = FALSE)
getRegionDNA(roi, genome, introns = FALSE)

Arguments

`roi`	`makeROI` object
`genome`	BSgenome object
`introns`	TRUE/FALSE. whether to include intronic (lowercase) DNA. By default returns only exonic (uppercase) DNA.

Value

list of
(1) DNA sequence (2) Junction start (for primer design)

Author(s)

Diana Low

Examples

suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
getRegionDNA(roi,bsgenome)
suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
getRegionDNA(roi,bsgenome)

insertRegion

Description

inserts a region (exon or intron) into roi object

Usage

insertRegion(subject, roi)
insertRegion(subject, roi)

Arguments

`subject`	GrangesList
`roi`	`makeROI` object containg region of interest (to insert). refer to makeROI().

Details

in the case of intron retention, replaces exon with intron retention range reduce() the GRanges in question

Value

GRanges object

Author(s)

Diana Low

Examples

#Inserts the exon defined in roi GRanges object from a GRanges/GRangesList
region_minus_exon
region_with_exon<-insertRegion(region_minus_exon,roi)
#Inserts the exon defined in roi GRanges object from a GRanges/GRangesList
region_minus_exon
region_with_exon<-insertRegion(region_minus_exon,roi)

makeROI

Description

Creates an object to store information about the splice site (region of interest) including flanking regions and alternative splice outcome

Usage

makeROI(df, type = "SE")
makeROI(df, type = "SE")

Arguments

`df`	data.frame object from `extractSpliceEvents`
`type`	type of splicing event c("SE","RI","MXE","A5SS","A3SS")

Value

a list containing
(1) type : splice type
(2) name : ID of transcript
(3) roi : GRanges object of splice site
(4) flank : GRanges object of flanking exons of splice site
(5) roi_range : GRangesList of splice site and it's alternative outcome based on type

Author(s)

Diana Low

Examples

single_record<-splice_data$data[which(grepl("Prmt5",splice_data$data$Symbol)),]
roi <- makeROI(single_record,type="SE")
single_record<-splice_data$data[which(grepl("Prmt5",splice_data$data$Symbol)),]
roi <- makeROI(single_record,type="SE")

makeUniqueIDs

Description

Makes unique ID names from event location

Usage

makeUniqueIDs(ddata)
makeUniqueIDs(ddata)

Arguments

ddata

extractSpliceEvents object

Value

original extractSpliceEvents list object with unique ID appended to data accessor

Author(s)

Diana Low

Examples

data_with_id<-makeUniqueIDs(splice_data)
data_with_id<-makeUniqueIDs(splice_data)

pcr_result1

Description

pcr_result1

Examples

data(pcr_result1)
data(pcr_result1)

plotting sequence logo

Description

Plots the sequence logo of a given set of FASTA sequences

Usage

plot_seqlogo(fasta_seq)
plot_seqlogo(fasta_seq)

Arguments

fasta_seq

DNAStringSet or path to fasta-formatted file

Value

sequence logo image

Author(s)

Diana Low

Examples

head(splice_fasta)
plot_seqlogo(Biostrings::DNAStringSet(splice_fasta$V2))
head(splice_fasta)
plot_seqlogo(Biostrings::DNAStringSet(splice_fasta$V2))

primers

Description

primers designed using Primer3 for sample data

Usage

data("primers")data("primers")

Format

A data frame with 5 observations on the following 28 variables.

i: a numeric vector
PRIMER_LEFT_SEQUENCE: a character vector
PRIMER_RIGHT_SEQUENCE: a character vector
PRIMER_LEFT_TM: a numeric vector
PRIMER_RIGHT_TM: a numeric vector
PRIMER_LEFT_pos: a numeric vector
PRIMER_LEFT_len: a numeric vector
PRIMER_RIGHT_pos: a numeric vector
PRIMER_RIGHT_len: a numeric vector
PRIMER_PAIR_PENALTY: a numeric vector
PRIMER_LEFT_PENALTY: a numeric vector
PRIMER_RIGHT_PENALTY: a numeric vector
PRIMER_LEFT_GC_PERCENT: a numeric vector
PRIMER_RIGHT_GC_PERCENT: a numeric vector
PRIMER_LEFT_SELF_ANY_TH: a numeric vector
PRIMER_RIGHT_SELF_ANY_TH: a numeric vector
PRIMER_LEFT_SELF_END_TH: a numeric vector
PRIMER_RIGHT_SELF_END_TH: a numeric vector
PRIMER_LEFT_HAIRPIN_TH: a numeric vector
PRIMER_RIGHT_HAIRPIN_TH: a numeric vector
PRIMER_LEFT_END_STABILITY: a numeric vector
PRIMER_RIGHT_END_STABILITY: a numeric vector
PRIMER_LEFT_TEMPLATE_MISPRIMING: a numeric vector
PRIMER_RIGHT_TEMPLATE_MISPRIMING: a numeric vector
PRIMER_PAIR_COMPL_ANY_TH: a numeric vector
PRIMER_PAIR_COMPL_END_TH: a numeric vector
PRIMER_PAIR_PRODUCT_SIZE: a numeric vector
PRIMER_PAIR_TEMPLATE_MISPRIMING: a numeric vector

Value

Dataframe of primer design results

Examples

data(primers)
data(primers)

psiPlot

Description

Plots percentage spliced in (PSI) values in terms of inclusion levels

Usage

psiPlot(df = NULL, type = "MATS", sample_labels = c("Sample 1", "Sample 2"))
psiPlot(df = NULL, type = "MATS", sample_labels = c("Sample 1", "Sample 2"))

Arguments

`df`	data.frame containing PSI values
`type`	character. either 'MATS' output (will read in MATS headers) or 'generic' (provide 4 or 6 column data.frame)
`sample_labels`	x-axis labels for the plot

Value

bar plot of PSI values

Author(s)

Diana Low

Examples

#we give inclusion and skipped numbers as reads
#this will be converted into percentages
df<-data.frame(inclusion1=c("6,4,6"),skipped1=c("10,12,12"),inclusion2=c("15,15,15"),
     skipped2=c("3,3,4"),stringsAsFactors = FALSE)
psiPlot(df,type='generic')

#we give inclusion and skipped numbers as reads
#this will be converted into percentages
df<-data.frame(inclusion1=c("6,4,6"),skipped1=c("10,12,12"),inclusion2=c("15,15,15"),
     skipped2=c("3,3,4"),stringsAsFactors = FALSE)
psiPlot(df,type='generic')

region_minus_exon

Description

region_minus_exon

Examples

data(region_minus_exon)
## maybe str(region_minus_exon) ; plot(region_minus_exon) ...
data(region_minus_exon)
## maybe str(region_minus_exon) ; plot(region_minus_exon) ...

removeRegion

Description

removes a region (exon) from a GRanges or GRangesList

Usage

removeRegion(subject, roi)
removeRegion(subject, roi)

Arguments

`subject`	GRanges or GrangesList object
`roi`	`makeROI` object containing GRanges range (to remove)

Value

GRanges object

Author(s)

Diana Low

# Removes the exon defined in roi GRanges object from a GRanges/GRangesList compatible_cds$hits[[1]] region_minus_exon<-removeRegion(compatible_cds$hits[[1]],roi)

roi

Description

roi

Usage

data("roi")data("roi")

Value

List containing region of interest information

Examples

data(roi)
data(roi)

shapiroAcceptor

Description

Shapiro's score of acceptor site (range is from -13 [intron] to +1 [exon]) is: 100 * ((t1 - l1)/(h1 - l1) + (t2 - l2)/(h2 - l2))/2, where t1 is the sum of the best 8 of 10 percentages at positions -13 to -4, l1 is the sum of the lowest 8 of 10 percentages at position -13 to -4, h1 is the sum of the highest 8 of 10 percentages at positions -13 to -4, t2 is the sum of percentages at positions -3 to +1, l2 is the sum of the lowest percentages at positions -3 to +1, and h2 is the sum of the highest percentages at positions -3 to +1

Usage

shapiroAcceptor(reference_fasta, target_fasta)
shapiroAcceptor(reference_fasta, target_fasta)

Arguments

`reference_fasta`	vector of strings or DNAStringSet of reference splice list
`target_fasta`	vector of strings or DNAStringSet of fasta to score

Value

data.frame with Shapiro scores

Author(s)

Diana Low

Examples

library(BSgenome.Mmusculus.UCSC.mm9)
bsgenome <- BSgenome.Mmusculus.UCSC.mm9
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data,site="acceptor")
acceptor.ss<-getSeq(bsgenome,splice_sites)
##sacceptor<-shapiroAcceptor(acceptor.m,acceptor.ss)
library(BSgenome.Mmusculus.UCSC.mm9)
bsgenome <- BSgenome.Mmusculus.UCSC.mm9
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data,site="acceptor")
acceptor.ss<-getSeq(bsgenome,splice_sites)
##sacceptor<-shapiroAcceptor(acceptor.m,acceptor.ss)

shapiroDensity

Description

convenience function for plotting Shapiro score density

Usage

shapiroDensity(ctrl_scores, treat_scores, sample = c(1, 2))
shapiroDensity(ctrl_scores, treat_scores, sample = c(1, 2))

Arguments

`ctrl_scores`	output of shapiroDonor or shapiroAcceptor
`treat_scores`	output of shapiroDonor or shapiroAcceptor
`sample`	samplenames

Value

density plot of Shapiro scores

Author(s)

Diana Low

shapiroDonor

Description

Shapiro and Senapathy (1987) have developed a method to score the strength of a splice site based on percentages of each nucleotide at each position. Shapiro's score of donor site (range is from -3 [exon] to +7 [intron]) is : 100 * (t - min)/ (max - min), where t is the sum of percentages at positions -3 to +7, min is the sum of the lowest percentages at positions -3 to +7, and max is the sum of the highest percentages at positions -3 to +7.

Usage

shapiroDonor(reference_fasta, target_fasta)
shapiroDonor(reference_fasta, target_fasta)

Arguments

`reference_fasta`	vector of strings or DNAStringSet of reference splice list
`target_fasta`	vector of strings or DNAStringSet of fasta to score

Value

data.frame with Shapiro scores

Author(s)

Diana Low

Examples

library(BSgenome.Mmusculus.UCSC.mm9)
bsgenome <- BSgenome.Mmusculus.UCSC.mm9
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data)
donor.ss<-getSeq(bsgenome,splice_sites)
##sdonor<-shapiroDonor(donor.m,donor.ss)
library(BSgenome.Mmusculus.UCSC.mm9)
bsgenome <- BSgenome.Mmusculus.UCSC.mm9
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data)
donor.ss<-getSeq(bsgenome,splice_sites)
##sdonor<-shapiroDonor(donor.m,donor.ss)

splice_data

Description

splice_data

Usage

data("splice_data")data("splice_data")

Value

List containing splice event file information

Examples

data(splice_data)
data(splice_data)

splice_fasta

Description

splice_fasta

Usage

data("splice_fasta")data("splice_fasta")

Format

A data frame with 0 observations on the following 2 variables.

V1: a numeric vector
V2: a numeric vector

Value

Dataframe of region and fasta sequence

Examples

data(splice_fasta)
data(splice_fasta)

splitPCRhit

Description

splits the PCR alignment into the two AS conditions

Usage

splitPCRhit(res, hitlist)
splitPCRhit(res, hitlist)

Arguments

`res`	result from `getPCRsizes`
`hitlist`	`findCompatibleEvents` object

Value

list of 2 data.frame objects with isoform name (ID) and length of PCR product (bp) matching Type 1 or Type 2 transcripts

Author(s)

Diana Low

Examples

## as getPCRsizes gives you all PCR bands when the primers are used,
## splitPCRhit will determine which bands are relevant to the target
relevant_pcr_bands<-splitPCRhit(pcr_result1,compatible_tx)
## as getPCRsizes gives you all PCR bands when the primers are used,
## splitPCRhit will determine which bands are relevant to the target
relevant_pcr_bands<-splitPCRhit(pcr_result1,compatible_tx)

thecds

Description

thecds

Usage

data("thecds")data("thecds")

Value

List containing GRanges info

Examples

data(thecds)
data(thecds)

theexons

Description

theexons

Usage

data("thecds")data("thecds")

Value

List containing GRanges info

Examples

data(theexons)
data(theexons)

valid_cds

Description

valid_cds

Usage

data("valid_cds")data("valid_cds")

Value

GRangesList

Examples

data(valid_cds)
data(valid_cds)

valid_tx

Description

valid_tx

Value

GRangesList

Examples

data(valid_tx)
## maybe str(valid_tx) ; plot(valid_tx) ...
data(valid_tx)
## maybe str(valid_tx) ; plot(valid_tx) ...

Package 'SPLINTER'

Help Index

acceptor.m

Description

Usage

Format

Source

References

Examples

addEnsemblAnnotation

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

annotateEvents

Description

Usage

Arguments

Value

Author(s)

callPrimer3

Description

Usage

Arguments

Details

Value

Author(s)

Examples

checkPrimer

Description

Usage

Arguments

Value

Author(s)

Examples

compatible_cds

Description

Examples

compatible_tx

Description

Examples

donor.m

Description

Usage

Format

Source

References

Examples

eventOutcomeCompare

Description

Usage

Arguments

Value

Author(s)

Examples

eventOutcomeTranslate

Description

Usage

Arguments

Value

Author(s)

Examples

eventPlot

Description

Usage

Arguments

Value

Author(s)

Examples

extendROI

Description

Usage

Arguments

Value

Examples

extractSpliceEvents

Description