normalize: normalize

In stasaki/Guitar: Guitar

Description

This function Comparing the sampled site with the normalized guitar coordinate system to find the relative position of each site in the zero to one coordinate system, and calculating the weight of each site at this position.

Usage

normalize(sitesGRanges, 
          guitarTxdb, 
          txType,
          overlapIndex,
          siteLengthIndex)

Arguments

sitesGRanges	A kind of GRange object, generated by sampling the site.
guitarTxdb	Sites mapping on guitartxdb and finding the corresponding location on the transcript.
txType	Transcript type comparing with guitar coordinate's transcript type.
overlapIndex	Index of site overlapping times. Default: 1.
siteLengthIndex	Index of site length. Default: 1.

Value

A data list object contains two types of data information, one is the location information of the site, and the other is the weight information of the site.

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))
# read transcript information
txdb_file <- system.file("extdata", "mm10_toy.sqlite", package="Guitar")
txdb <- loadDb(txdb_file)
guitarTxdb <- makeGuitarTxdb(txdb) 
sitesGRanges <- samplePoints(list(site), 
                            stSampleNum = 5,
                            stAmblguity = 5,
                            pltTxType = c("mrna"),
                            stSampleModle = "Equidistance",
                            mapFilterTranscript = FALSE,
                            guitarTxdb)
sitesNormlize <- normalize(sitesGRanges, 
                           guitarTxdb, 
                           txType = "mrna",
                           overlapIndex = 1,
                           siteLengthIndex = 1)

stasaki/Guitar documentation built on Feb. 5, 2021, 12:21 p.m.