act (version 1.3.1)

transcripts_cure_single: Cure a single transcript

Description

Transcript object may contain errors, e.g. because of defect annotation input files or user modifications. This function may cure some of these errors.

• Annotations with reversed times: annotations with endSec lower than startSec will be deleted.

• Overlapping annotations: earlier annotations will end where the next annotation starts.

• Annotations below 0 sec: Annotations that are starting and ending before 0 sec will be deleted; Annotations starting before but ending after 0 sec will be truncated.

• Missing tiers: Tiers that are present in the annotations but missing in the list of tiers in @tiers of the transcript object will be added.

Usage

transcripts_cure_single(
  t,
  annotationsWithReversedTimes = TRUE,
  overlappingAnnotations = TRUE,
  annotationsWithTimesBelowZero = TRUE,
  missingTiers = TRUE,
  showWarning = FALSE
)

Value

Transcript object;

Arguments

t

Transcript object.

annotationsWithReversedTimes

Logical; If TRUE annotations with reversed times will be deleted

overlappingAnnotations

Logical; If TRUE overlapping annotations will be corrected.

annotationsWithTimesBelowZero

Logical; If TRUE annotations before 0 sec will be corrected.

missingTiers

Logical; If TRUE tiers missing in @tiers slot of the transcript object will be added.

showWarning

Logical; If TRUE a warning notice will be shown upon correction.

See Also

transcripts_cure

Examples

library(act)

# --- annotationsWithReversedTimes: will be deleted
# get example transcript and reverse the times of an annotation
t <- examplecorpus@transcripts[[1]]
t@annotations$startSec[1] <- 20
t@annotations$endSec[1] <- 10
t2 <- act::transcripts_cure_single(t)
tail(t2@history, n=1)


# --- annotationsWithTimesBelowZero: will be deleted or start at 0 sec
t <- examplecorpus@transcripts[[1]]
t@annotations$startSec[1] <- -2
t@annotations$endSec[1]   <- -1
t2 <- act::transcripts_cure_single(t)
tail(t2@history, n=1)

t <- examplecorpus@transcripts[[1]]
t@annotations$startSec[2] <- -5
t2 <- act::transcripts_cure_single(t)
tail(t2@history, n=1)


# --- overlappingAnnotations: will end where the next starts
t<- examplecorpus@transcripts[[1]]
t@annotations <- t@annotations[order(t@annotations$tier.name, t@annotations$startSec), ]
t@annotations$endSec[1] <- 8
t2 <- act::transcripts_cure_single(t)
tail(t2@history, n=1)


# --- missingTiers: will be added to @tiers in transcript object
t<- examplecorpus@transcripts[[1]]
t@annotations <- t@annotations[order(t@annotations$tier.name, t@annotations$startSec), ]
t@annotations$tier.name[1] <- "NEW"
t2 <- act::transcripts_cure_single(t)
tail(t2@history, n=1)
t2@tiers
# compare with original tiers
t@tiers


# --- several things at once
t<- examplecorpus@transcripts[[1]]
t@annotations <- t@annotations[order(t@annotations$tier.name, t@annotations$startSec), ]
# annotation completely below 0 sec
t@annotations$startSec[1] <- -6
t@annotations$endSec[1]   <- -5
# annotation starts before but ends after 0 sec
t@annotations$startSec[2] <- -3
# annotation with reversed times
t@annotations$startSec[3] <- 6.9
t@annotations$endSec[3]   <- -6.8
# annotation overlaps with next annotation
t@annotations$endSec[6]   <- 9
# new tier, missing tier list
t@annotations$tier.name[8] <- "NEW"
t2 <- act::transcripts_cure_single(t, showWarning=TRUE)
tail(t2@history, n=1)


examplecorpus@transcripts[[1]]@history