Function importing data from bedgraph format compatible with UCSC Genome
Browser to norm_GR data frame. Warning: Compatible only with bedgraph files
generated by norm2bedgraph function (bedgraph needs to have 2 tracks, first
for plus strand, second for minus strand). May be used for transforming
normalized data to another different annotation sets.
path to fasta file which is used for a) choosing which
transcripts to use (transcripts absent from fasta are not reported), b)
providing sequence for to display in GRanges metadata
txDb
TranscriptDb object with transcript definitions. Names must
match those in fasta_file
bed_file
character containing file path to BED file with transcript
definitions. Supply txDb XOR bedfile
column_name
How to name imported metadata in GRanges
add_to
GRanges object made by other normalization function (dtcr(),
slograt(), swinsor(), compdata()) to which values from bedgraph should be
added.
track_strand
specifies which genomic strand the supplied bedgraph
describes ("+" or "-"). Used only if the bedgraph file is composed of only
one track.
Value
Function creates GRanges object or (if add_to specified) adds
metadata to already existing object
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(RNAprobR)
Loading required package: GenomicFeatures
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: GenomicRanges
Loading required package: AnnotationDbi
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: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAprobR/bedgraph2norm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bedgraph2norm
> ### Title: Import bedgraph to GRanges
> ### Aliases: bedgraph2norm
>
> ### ** Examples
>
> dummy_euc_GR_control <- GRanges(seqnames="DummyRNA",
+ IRanges(start=round(runif(100)*100), width=round(runif(100)*100+1)),
+ strand="+", EUC=round(runif(100)*100))
> dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
+ IRanges(start=round(runif(100)*100),
+ width=round(runif(100)*100+1)),
+ strand="+", EUC=round(runif(100)*100))
> dummy_comp_GR_control <- comp(dummy_euc_GR_control)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_norm <- dtcr(control_GR=dummy_comp_GR_control,
+ treated_GR=dummy_comp_GR_treated)
>
> write(strwrap("chr1\t134212702\t134229870\tDummyRNA\t0\t+
+ \t134212806\t134228958\t0\t8\t347,121,24,152,66,120,133,1973,
+ \t0,8827,10080,11571,12005,13832,14433,15195,", width = 300),
+ file="dummy.bed")
> norm2bedgraph(norm_GR = dummy_norm, bed_file = "dummy.bed")
Warning: normalization method to convert not specified. dtcr chosen.
Warning message:
Using togroup() on a CompressedIRangesList object is deprecated. Please
use togroup(PartitioningByWidth(...)) instead.
>
> write(c(">DummyRNA", paste(sample(c("A","C","G","T"), 100, replace=TRUE),
+ collapse="")), file="dummy.fa")
> bedgraph2norm(bedgraph_file = "out_file.bedgraph", fasta_file = "dummy.fa",
+ bed_file = "dummy.bed")
For RNA DummyRNA positions outside FASTA annotation exist. N's added
GRanges object with 189 ranges and 2 metadata columns:
seqnames ranges strand | nt bedgraph_score
<Rle> <IRanges> <Rle> | <character> <numeric>
DummyRNA.1 DummyRNA [1, 1] + | C 0.3333333
DummyRNA.2 DummyRNA [2, 2] + | A 0.5460317
DummyRNA.3 DummyRNA [3, 3] + | A 0.3342521
DummyRNA.4 DummyRNA [4, 4] + | A 0.3757211
DummyRNA.5 DummyRNA [5, 5] + | T 0.2265148
... ... ... ... . ... ...
DummyRNA.185 DummyRNA [185, 185] + | N 0
DummyRNA.186 DummyRNA [186, 186] + | N 0
DummyRNA.187 DummyRNA [187, 187] + | N 0
DummyRNA.188 DummyRNA [188, 188] + | N 0
DummyRNA.189 DummyRNA [189, 189] + | N 0
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
Warning messages:
1: In asMethod(object) : NAs introduced by coercion
2: Using togroup() on a CompressedIRangesList object is deprecated. Please
use togroup(PartitioningByWidth(...)) instead.
>
>
>
>
>
> dev.off()
null device
1
>