norm2bedgraph {RNAprobR} | R Documentation |
Function converts annotation from transcript to genomic coordinates and creates two-track bedgraph file (one track for each strand)
norm2bedgraph(norm_GR, txDb, bed_file, norm_method, genome_build, bedgraph_out_file = "out_file", track_name = "Track_name", track_description = "Track_description")
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 |
Function writes bedgraph file.
Lukasz Jan Kielpinski, Nikos Sidiropoulos
bedgraph2norm
, norm_df2GR
,
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")