Description Usage Arguments Value Author(s) See Also Examples
View source: R/bedgraph2norm.R
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.
1 2 | bedgraph2norm(bedgraph_file, fasta_file, txDb, bed_file,
column_name = "bedgraph_score", add_to, track_strand = "+")
|
bedgraph_file |
path to compatible bedgraph file |
fasta_file |
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. |
Function creates GRanges object or (if add_to specified) adds metadata to already existing object
Lukasz Jan Kielpinski, Nikos Sidiropoulos
norm2bedgraph
, GR2norm_df
,
plotRNA
, BED2txDb
, dtcr
,
slograt
, swinsor
, compdata
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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)
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
dummy_norm <- dtcr(control_GR=dummy_comp_GR_control,
treated_GR=dummy_comp_GR_treated)
write(paste(c("chr1", 134212702, 134229870, "DummyRNA", 0, "+", 134212806,
134228958, 0, 8, "347,121,24,152,66,120,133,1973,",
"0,8827,10080,11571,12005,13832,14433,15195,"), collapse = "\t"),
file="dummy.bed")
norm2bedgraph(norm_GR = dummy_norm, bed_file = "dummy.bed")
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")
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