read_annotated_ampliseq_amplicons: Read AmpliSeq amplicon informaiton from an annotated BED file

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

Read AmpliSeq amplicon informaiton from an annotated BED file

Description

Read AmpliSeq amplicon informaiton from an annotated BED file

Usage

read_annotated_ampliseq_amplicons(bedFile)

Arguments

bedFile

Character string, an annotated BED file with Gene_ID (gene symbols) and EntrezGeneID (Entrez Gene IDs) in the eighth column.

Value

A data.frame, besides reporting the columns in the BED file, contains following additional annotation information:

1. Amplicon

2. GeneID

3. GeneSymbol

4. RefSeq

5. Length

Note

There are several versions of BED file used. This function works only with the latest version.

See Also

read_bed

Examples

lines <- paste0("#track type=bedDetail ionVersion=4.0 name=\"IAD50039-4_IAD87652-4_Design\"",
 "solution_type=4 description=\"TargetRegions_AmpliSeqID_IAD50039 AmpliSeq_Version=3.0.1",
 " Workflow=RNA merged with TargetRegions_AmpliSeqID_IAD87652 AmpliSeq_Version=4.48 Workflow=RNA\"",
 " color=77,175,74 priority=2", "\n",
 "NM_000014\t3316\t3421\tAMPL1384\t.\tGENE_ID=A2M;EntrezGeneID=2", "\n",
 "NM_005502\t2488\t2589\tAMPL28385508\t.\tGENE_ID=ABCA1;EntrezGeneID=19","\n",
 "NM_000927\t2520\t2624\tAMPL5599607\t.\tGENE_ID=ABCB1;EntrezGeneID=5243","\n",
 "NM_000443\t1367\t1470\tAMPL5513474\t.\tGENE_ID=ABCB4;EntrezGeneID=5244")
 read_annotated_ampliseq_amplicons(textConnection(lines))

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