samplePoints: samplePoints

In Guitar: Guitar

Description

This function calculates the length of each sites and then samples the points from sites by using two sampling methods based on the number of sampling points. One sampling method is equidistant sampling, the N sampling points are sampled at equal intervals according to the length of the site. Another method is random sampling, and N sampling points are randomly distributed on the site.

Usage

samplePoints(sitesGrangelists, 
             stSampleNum = 5,
             stAmblguity = 5,
             pltTxType = c("tx","mrna","ncrna"),
             stSampleModle = "Equidistance",
             mapFilterTranscript = FALSE,
             guitarTxdb)
            

Arguments

sitesGrangelists	A GRangeslist object, the content of the sites information.
stSampleNum	The number of bases sampled at each Site. Default: 3.
stAmblguity	Maximum overlap between sites. Default: 5.
pltTxType	Transcript type mapped to guitartxdb.
stSampleModle	sampling "Equidistance",sampling "random". Default:"Equidistance".
mapFilterTranscript	Whether to filter the length of transcripts equal the original site. Default: FALSE.
guitarTxdb	Sites mapping on guitartxdb and finding the corresponding location on the transcript.

Value

A GRange data list, the content of the list is the sampling point, the width is 1, the total number of data is N times the input data.

Author(s)

Xiao Du<[e-mail]>

Examples

# read genomic features
stBedFile <- system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed", package="Guitar")
site <-  blocks(import(stBedFile))
#generate GuitarTxdb
txdb_file <- system.file("extdata", "mm10_toy.sqlite", package="Guitar")
txdb <- loadDb(txdb_file)
guitarTxdb <- makeGuitarTxdb(txdb) 
# sample site points
sitesPoints <- samplePoints(list(site), 
                            stSampleNum = 5,
                            stAmblguity = 5,
                            pltTxType = c("tx","mrna","ncrna"),
                            stSampleModle = "Equidistance",
                            mapFilterTranscript = FALSE,
                            guitarTxdb)

Guitar documentation built on Nov. 8, 2020, 5:15 p.m.