norm2bedgraph: Exporting data in norm_df data frame (product of dtcr,...

In RNAprobR: An R package for analysis of massive parallel sequencing based RNA structure probing data

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.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

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(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")

RNAprobR documentation built on Nov. 8, 2020, 5:57 p.m.