RNAprobR (version 1.4.0)

norm2bedgraph: Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser

Description

Function converts annotation from transcript to genomic coordinates and creates two-track bedgraph file (one track for each strand)

Usage

norm2bedgraph(norm_GR, txDb, bed_file, norm_method, genome_build, bedgraph_out_file = "out_file", track_name = "Track_name", track_description = "Track_description")

Arguments

norm_GR

norm_GR GRanges with data to be exported, required

txDb

TranscriptDb object with transcript definitions. Names must match those in norm_df

bed_file

character containing file path to BED file with transcript definitions. Supply txDb XOR bedfile

norm_method

character specifying which normalized column should be processed into bedgraph. If not provided, the first column matching dtcr, slograt or swinsor is transformed.

genome_build

character specifying which UCSC genome build should data be displayed in, e.g. "mm9"

bedgraph_out_file

character specifying prefix of output file. Generated file name is: prefix.bedgraph; if file with such a name already exists new tracks will be appended.

track_name

character specifying track name

track_description

character specifying track description

Value

Function writes bedgraph file.

See Also

bedgraph2norm, norm_df2GR, dtcr, slograt, swinsor, compdata

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)
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(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")