getMotifStutterInfo: getMotifStutterInfo

In Mariamsp/brackconv: What the Package Does (One Line, Title Case)

getMotifStutterInfo

Description

Creates final table with stutter information

Usage

getMotifStutterInfo(
  seqBrack,
  addSeq1Coverage = TRUE,
  addSeq2Coverage = TRUE,
  addSeq1allele_type = TRUE,
  addSeq2allele_type = TRUE,
  addSeq1SequenceID = TRUE,
  addSeq2SequenceID = TRUE,
  addSeq1ATcontent = TRUE,
  addSeq2ATcontent = TRUE,
  addStutterProportion = TRUE
)

Arguments

seqBrack	matrix with STRs sequence converted into bracket format, reads, allele_type, Sequence ID and AT-content
addSeq1Coverage	TRUE condition for adding Seq1 read counts ("coverage") to the final stutter table
addSeq2Coverage	TRUE condition for adding Seq2 read counts to the final stutter table
addStutterProportion	TRUE condition for adding the stutter proportion to the stutter table. Proportion of read counts Seq2 compare to the total (Seq1 + Seq2)

Details

Help function. Takes as input the short bracket format sequences. Compares one sequence with the remaining sequences by extracting and comparing their repetitive motifs. If equal, then number of repetitions of the motifs will be compared and variations will be considered as stutters.

NOTE: STUTTER PRODUCTS ARE ASSUMED TO NOT EXCEED THE COMPARING SEQUENCE

Value

data frame with sequences Seq1 and Seq2, number of different motifs (motifDifference), read counts (coverage) for Seq1 and Seq2, and stutter proportion.

Author(s)

Oyvind Bleka <oyvble.at.hotmail.com>

Examples

## Not run: 
bracketformat <- c("[ATCT]12","[ATCT]10", "[ATCT]11", "[ATCT]9")
reads <- c(869, 60, 28, 23)
allele_type <- c(1,2,3,3)
Sequence_ID <- c(227760, 227761, 227762,227763)
AT_contentVar <- c(75.00, 33.33, 64.00, 77.33)
seqBrack <- rbind(reads, allele_type, Sequence_ID, AT_contentVar)
colnames(seqBrack) <- bracketformat
getMotifStutterInfo(seqBrack)
## End(Not run)

Mariamsp/brackconv documentation built on March 17, 2022, 5:14 p.m.