write_annotated_ampliseq_amplicons: Write AmpliSeq amplicon informaiton into an annotated BED...

In ribiosIO: Input/Output Utilities of the 'ribios' Suite

Write AmpliSeq amplicon informaiton into an annotated BED file

Description

Write AmpliSeq amplicon informaiton into an annotated BED file

Usage

write_annotated_ampliseq_amplicons(
  df,
  bedFile,
  version = format(Sys.time(), "%Y%m%d")
)

Arguments

df	A data.frame containing following columns (names do not matter): chrom (RefSeq IDs) chromStart (integer) chromEnd (integer) name (Amplicon IDs) score (A single value, .) ID (in the format of GENE_ID=$GENESYMBOL;EntrezGeneID=$EG_ID)
bedFile	Character string, the output file
version	Character string, a version number. By default, the current date is used.

Value

No return value, called for side effects (writes an annotated BED file).

See Also

read_annotated_ampliseq_amplicons

Examples

mydf <- data.frame(chrom=c("NM_000014", "NM_000015", "NM_000021"),
  chromStart=c(3316, 50, 1212),
  chromEnd=c(3421, 146, 1320),
  name=c("AMPL1384", "AMPL7195", "AMPL14470"),
  score=".",
  ID=c("GENE_ID=A2M;EntrezGeneID=2",
       "GENE_ID=NAT2;EntrezGeneID=10",
       "GENE_ID=PSEN1;EntrezGeneID=5663"))
myBed <- tempfile()  
write_annotated_ampliseq_amplicons(mydf, myBed)
mydfOut <- read_annotated_ampliseq_amplicons(myBed)

ribiosIO documentation built on Feb. 20, 2026, 5:09 p.m.