read_ampliseq_bedcovgct: Read bedcov output of AmpliSeq amplicons and convert them to...

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

Read bedcov output of AmpliSeq amplicons and convert them to read counts

Description

Read bedcov output of AmpliSeq amplicons and convert them to read counts

Usage

read_ampliseq_bedcovgct(file, bedFile)

Arguments

file	Character string, a GCT file containing bedcov output of amplicons
bedFile	Character string, an annotated BED file encoding amplicons

Value

A GctMatrix object containing read counts

The function is used to convert read base counts returned by samtools bedcov to read counts using Amplicon information encoded in the bed file

See Also

read_annotated_ampliseq_amplicons

Examples

bedlines <- 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")
 gctLines <- paste0("#1.2", "\n",
 "3\t3","\n",
 "NAME\tDescription\tS1\tS2\tS3","\n",
 "A2M\tNM_000014\t105\t210\t315", "\n",
 "ABCA1\tNM_005502\t202\t303\t404", "\n",
 "ABCB1\tNM_000927\t312\t416\t520")
 bedcovGct <- read_ampliseq_bedcovgct(textConnection(gctLines), 
   textConnection(bedlines))
 bedcovGct

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