buildSsTypePwms: Building Position Weight Matrices for Splice Sites of U12 and...
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Value Author(s) See Also Examples

Builds position Weigh Matrices for the donor and acceptor sites of the U12 and U2 type introns, and the branchpoint of the U12 type introns. if pdfFileSeqLogos is defined a pdf is also produced that contains the sequence logos of the results. The result is a list that contains PWMs of the splice sites of U12 and U2 dependent introns.

buildSsTypePwms( cexSeqLogo=1, pdfWidth=35, pdfHeight=10, tmpDir="./",
	u12dbSpecies="Homo_sapiens", 
	pwmSource="U12DB", 
	u12DonorBegin, u12BranchpointBegin, u12AcceptorBegin, 
	u2DonorBegin, u2AcceptorBegin, u12DonorEnd, 
	u12BranchpointEnd, u12AcceptorEnd, u2DonorEnd, 
	u2AcceptorEnd, pasteSites=FALSE,
	splicerackSsLinks=list(
		U12_AT_AC_donor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.25", 
		U12_AT_AC_branchpoint=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.26",
		U12_AT_AC_acceptor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.29",
		U12_GT_AG_donor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.22", 
		U12_GT_AG_branchpoint=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.27",
		U12_GT_AG_acceptor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.21",
		U2_GC_AG_donor="http://katahdin.mssm.edu/splice/out/9606_logo_file.24",
		U2_GC_AG_acceptor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.30", 
		U2_GT_AG_donor="http://katahdin.mssm.edu/splice/out/9606_logo_file.23",
		U2_GT_AG_acceptor=
			"http://katahdin.mssm.edu/splice/out/9606_logo_file.28"),
	u12dbLink="ftp://genome.imim.es/pub/software/u12/u12db_v1_0.sql.gz",
	u12dbDbName="u12db", u12dbDropDb=TRUE,  pdfFileSeqLogos="", 
	removeTempFiles=TRUE, ...)

`cexSeqLogo`	Font size of sequence logo plots; used only if `pdfFileSeqLogos` is defined.
`pdfWidth, pdfHeight`	The width and height of the graphics region of the pdf in inches. The default values are 35 and 10.
`tmpDir`	Path to directory used for storing temporary files.
`u12dbSpecies`	What species data to use when getting the data from the U12DB database (`pwmSource="U12DB"`).
`pwmSource`	The source used to buildSplice Sites of U12 and U2 type introns the PWM for U12 and U2 dependent introns. Default is `U12DB`; but also accepts `SpliceRack`.
`u12DonorBegin, u12DonorEnd`	Integer values. They correspond to the begin and end point of the donor sequences of U12-type introns to consider (optional).
`u12BranchpointBegin, u12BranchpointEnd`	Integer values. Begin and end points of the branch point sequences of U12-type introns (optional).
`u12AcceptorBegin, u12AcceptorEnd`	Integer values. Begin and end points of the acceptor sequences of U12-type introns (optional).
`u2DonorBegin, u2DonorEnd`	Integer values. Begin and end points of the donor sequences of U2-type introns (optional).
`u2AcceptorBegin, u2AcceptorEnd`	Integer values. Begin and end points of the acceptor sequences of U2-type introns (optional).
`pasteSites`	Logical. If TRUE the donor, branch point and acceptor seqs are pasted before a PWM is built; then the PWMs of each (donor, acceptor and bp) are assigned. If FALSE (default) the PWMs for each is built separately.
`splicerackSsLinks`	A list (or vector) that contains the SpliceRack URL links to the text files that contain Position Weigh Matrices of the splice sites of U12 and U2 introns. This parameter is used only when pwmSource="SpliceRack". You can get the links to PWM files from this URL (choose logo files with "File" links): http://katahdin.mssm.edu/splice/splice_matrix.cgi?database=spliceNew. The links should be defined in the following order: `U12_AT_AC_donor`, `U12_AT_AC_branchpoint`, `U12_AT_AC_acceptor`, `U12_GT_AG_donor`, `U12_GT_AG_branchpoint`, `U12_GT_AG_acceptor`, `U2_GC_AG_donor`, `U2_GC_AG_acceptor`, `U2_GT_AG_donor`, and `U2_GT_AG_acceptor`.
`u12dbLink`	A character string containing the URL for downloading the zipped MySQL dump file of the U12DB. Used when `pwmSource="U12DB"`.
`u12dbDbName`	Name of the database copy of the U12DB that is build locally. Used when `pwmSource="U12DB"`.
`u12dbDropDb`	Drop (or remove) the local copy of the U12DB database at the end of the run. Used when `pwmSource="U12DB"`.
`pdfFileSeqLogos`	Path to PDF file containing the sequence logos of the results. By default it does not produce a file.
`removeTempFiles`	Whether remove temporary files at the end of the run; accepts `TRUE` or `FALSE` values (default is `TRUE`).
`...`	Authorization arguments needed by the DBMS instance. See the manual for `dbConnect` of the `DBI` package for more info.

`pwmDonorU12`	Matrix (with 4 rows represnting A, C, G, T and `n` columns representing the genomic coordinates) representing the Position Weight Matrix of donor site of U12-type introns.
`pwmBpU12`	Position Weight Matrix of branchpoint of U12-type introns.
`pwmAccU12`	Position Weight Matrix of acceptor site of U12-type introns.
`pwmDonU2`	Position Weight Matrix of donor site of U2-type introns.
`pwmAccU2`	Position Weight Matrix of acceptor site of U2-type introns.

Ali Oghabian

annotateU12.

# Time demanding function
## Not run: 
#Build temp directory  
tmpDir<- tempdir()


# Creating subdirectory for storing u12db temp files
dir.create(paste(tmpDir, "u12dbTmp", sep="/"))

# Extracting PWMs of Splice Sites of U12 and U2 type introns -
# based on u12db
u12dbPwm<-buildSsTypePwms(
	tmpDir=paste(tmpDir, "u12dbTmp", sep="/"),
	u12dbSpecies="Homo_sapiens",
	resource="U12DB",
	u12dbDbName="u12db",
	u12dbDropDb=TRUE,
	removeTempFiles=TRUE)


# Creating subdirectory for storing SpliceRack temp files
dir.create(paste(tmpDir, "splicerackTmp", sep="/"))

# Extracting PWMs of Splice Sites of U12 and U2 type introns - 
# based on SpliceRack
spliceRackPwm<- buildSsTypePwms(
	tmpDir= paste(tmpDir, "splicerackTmp", sep="/"),
	resource="SpliceRack",
	removeTempFiles=TRUE)

## End(Not run)