bedgraph2norm {RNAprobR} | R Documentation |
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.
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
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")