Last data update: 2014.03.03

 R: Count fragment overlaps
countFragmentOverlapsR Documentation

Count fragment overlaps

Description

countFragmentOverlaps counts the number of reads mapping to each fragment end in rowRanges of the FourC object.

Usage

countFragmentOverlaps(object, trim=0, minMapq=0, shift=0)

Arguments

object

A FourC object.

trim

Number of bases that should be trimmed at the start of a read. This is necessary if the read still contains the restriction enzyme sequence. Default is 0 bases.

minMapq

Minimum mapping quality required for counting the read. Default is 0. If set to negative values the filtering step is skipped.

shift

Maximum difference in starts or ends between read and fragment positions. Default is 0.

Value

Updated FourC object that contains two new assays countsLeftFragmentEnd and countsRightFragmentEnd with the count values at the respective fragment end.

Author(s)

Felix A. Klein, felix.klein@embl.de

See Also

FourC, findViewpointFragments, countFragmentOverlapsSecondCutter

Examples

metadata <- list(projectPath=tempdir(),
                 fragmentDir="re_fragments",
                 referenceGenomeFile=system.file("extdata/dm3_chr2L_1-6900.fa",
                                                 package="FourCSeq"),
                 reSequence1="GATC",
                 reSequence2="CATG",
                 primerFile=system.file("extdata/primer.fa",
                                        package="FourCSeq"),
                 bamFilePath=system.file("extdata/bam", package="FourCSeq"))

colData <- DataFrame(viewpoint = "testdata",
                     condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
                                            each=2),
                                        levels = c("WE_68h", "MESO_68h", "WE_34h")),
                     replicate = rep(c(1, 2),
                                     3),
                     bamFile = c("CRM_ap_ApME680_WE_6-8h_1_testdata.bam",
                                 "CRM_ap_ApME680_WE_6-8h_2_testdata.bam",
                                 "CRM_ap_ApME680_MESO_6-8h_1_testdata.bam",
                                 "CRM_ap_ApME680_MESO_6-8h_2_testdata.bam",
                                 "CRM_ap_ApME680_WE_3-4h_1_testdata.bam",
                                 "CRM_ap_ApME680_WE_3-4h_2_testdata.bam"),
                     sequencingPrimer="first")

fc <- FourC(colData, metadata)
fc

fc <- addFragments(fc)

findViewpointFragments(fc)

fc <- addViewpointFrags(fc)
fc

fc <- countFragmentOverlaps(fc, trim=4, minMapq=30)
fc

Results


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> library(FourCSeq)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: DESeq2
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: splines
Loading required package: LSD
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FourCSeq/countFragmentOverlaps.Rd_%03d_medium.png", width=480, height=480)
> ### Name: countFragmentOverlaps
> ### Title: Count fragment overlaps
> ### Aliases: countFragmentOverlaps
> 
> ### ** Examples
> 
> metadata <- list(projectPath=tempdir(),
+                  fragmentDir="re_fragments",
+                  referenceGenomeFile=system.file("extdata/dm3_chr2L_1-6900.fa",
+                                                  package="FourCSeq"),
+                  reSequence1="GATC",
+                  reSequence2="CATG",
+                  primerFile=system.file("extdata/primer.fa",
+                                         package="FourCSeq"),
+                  bamFilePath=system.file("extdata/bam", package="FourCSeq"))
> 
> colData <- DataFrame(viewpoint = "testdata",
+                      condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
+                                             each=2),
+                                         levels = c("WE_68h", "MESO_68h", "WE_34h")),
+                      replicate = rep(c(1, 2),
+                                      3),
+                      bamFile = c("CRM_ap_ApME680_WE_6-8h_1_testdata.bam",
+                                  "CRM_ap_ApME680_WE_6-8h_2_testdata.bam",
+                                  "CRM_ap_ApME680_MESO_6-8h_1_testdata.bam",
+                                  "CRM_ap_ApME680_MESO_6-8h_2_testdata.bam",
+                                  "CRM_ap_ApME680_WE_3-4h_1_testdata.bam",
+                                  "CRM_ap_ApME680_WE_3-4h_2_testdata.bam"),
+                      sequencingPrimer="first")
> 
> fc <- FourC(colData, metadata)
> fc
class: FourC 
dim: 0 6 
metadata(8): projectPath fragmentDir ... bamFilePath version
assays(0):
rownames: NULL
rowData names(0):
colnames(6): testdata_WE_68h_1 testdata_WE_68h_2 ... testdata_WE_34h_1
  testdata_WE_34h_2
colData names(5): viewpoint condition replicate bamFile
  sequencingPrimer
> 
> fc <- addFragments(fc)
> 
> findViewpointFragments(fc)
> 
> fc <- addViewpointFrags(fc)
> fc
class: FourC 
dim: 2 6 
metadata(8): projectPath fragmentDir ... bamFilePath version
assays(0):
rownames: NULL
rowData names(4): leftSize rightSize leftValid rightValid
colnames(6): testdata_WE_68h_1 testdata_WE_68h_2 ... testdata_WE_34h_1
  testdata_WE_34h_2
colData names(16): viewpoint condition ... primerEnd primerSide
> 
> fc <- countFragmentOverlaps(fc, trim=4, minMapq=30)
reading bam files
calculating overlaps
> fc
class: FourC 
dim: 2 6 
metadata(8): projectPath fragmentDir ... bamFilePath version
assays(2): countsLeftFragmentEnd countsRightFragmentEnd
rownames: NULL
rowData names(4): leftSize rightSize leftValid rightValid
colnames(6): testdata_WE_68h_1 testdata_WE_68h_2 ... testdata_WE_34h_1
  testdata_WE_34h_2
colData names(21): viewpoint condition ... mappedReads mappingRatio
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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