slideWindowTune - Parameter tuning for sliding window approach
Description¶
Apply slideWindowDb over a search grid made of combinations of mutThresh and
windowSize to help with picking a pair of values for these parameters. Parameter
tuning can be performed by choosing a combination that gives a reasonable number of
filtered/remaining sequences.
Usage¶
slideWindowTune(
db,
sequenceColumn = "sequence_alignment",
germlineColumn = "germline_alignment_d_mask",
dbMutList = NULL,
mutThreshRange,
windowSizeRange,
verbose = TRUE,
nproc = 1
)
Arguments¶
- db
data.framecontaining sequence data.- sequenceColumn
- name of the column containing IMGT-gapped sample sequences.
- germlineColumn
- name of the column containing IMGT-gapped germline sequences.
- dbMutList
- if supplied, this should be a list consisting of
data.frames returned as$posin the nested list produced by calcObservedMutations withreturnRaw=TRUE; otherwise, calcObservedMutations is called on columnssequenceColumnandgermlineColumnofdb. Default isNULL. - mutThreshRange
- range of threshold on the number of mutations in
windowSizeconsecutive nucleotides to try. Must be between 1 and maximumwindowSizeRangeinclusive. - windowSizeRange
- range of length of consecutive nucleotides to try. The lower end must be at least 2.
- verbose
- whether to print out messages indicating current progress. Default
is
TRUE. - nproc
- Number of cores to distribute the operation over. If the
clusterhas already been set earlier, then pass thecluster. This will ensure that it is not reset.
Value¶
a list of logical matrices. Each matrix corresponds to a windowSize in
windowSizeRange. Each column in a matrix corresponds to a mutThresh in
mutThreshRange. Each row corresponds to a sequence. TRUE values
mean the sequences has at least the number of mutations specified in the column name,
for that windowSize.
Details¶
If, in a given combination of mutThresh and windowSize, mutThresh
is greater than windowSize, NAs will be returned for that particular
combination. A message indicating that the combination has been “skipped” will be
printed if verbose=TRUE.
If calcObservedMutations was previously run on db and saved, supplying
$pos from the saved result as dbMutList could save time by skipping a
second call of calcObservedMutations. This could be helpful especially when
db is large.
Examples¶
# Load and subset example data
data(ExampleDb, package="alakazam")
db <- ExampleDb[1:5, ]
# Try out thresholds of 2-4 mutations in window sizes of 7-9 nucleotides.
# In this case, all combinations are legal.
slideWindowTune(db, mutThreshRange=2:4, windowSizeRange=7:9)
Identifying mutated positions
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Analyzing combinations of windowSizeRange and mutThreshRange
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$`7`
2 3 4
[1,] TRUE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] TRUE FALSE FALSE
[4,] TRUE FALSE FALSE
[5,] FALSE FALSE FALSE
$`8`
2 3 4
[1,] TRUE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] TRUE FALSE FALSE
[4,] TRUE FALSE FALSE
[5,] FALSE FALSE FALSE
$`9`
2 3 4
[1,] TRUE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] TRUE FALSE FALSE
[4,] TRUE FALSE FALSE
[5,] FALSE FALSE FALSE
# Illegal combinations are skipped, returning NAs.
slideWindowTune(db, mutThreshRange=2:4, windowSizeRange=2:4,
verbose=FALSE)
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$`2`
2 3 4
[1,] FALSE NA NA
[2,] FALSE NA NA
[3,] FALSE NA NA
[4,] FALSE NA NA
[5,] FALSE NA NA
$`3`
2 3 4
[1,] FALSE FALSE NA
[2,] FALSE FALSE NA
[3,] TRUE FALSE NA
[4,] TRUE FALSE NA
[5,] FALSE FALSE NA
$`4`
2 3 4
[1,] TRUE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] TRUE FALSE FALSE
[4,] TRUE FALSE FALSE
[5,] FALSE FALSE FALSE
# Run calcObservedMutations separately
exDbMutList <- sapply(1:5, function(i) {
calcObservedMutations(inputSeq=db[["sequence_alignment"]][i],
germlineSeq=db[["germline_alignment_d_mask"]][i],
returnRaw=TRUE)$pos })
slideWindowTune(db, dbMutList=exDbMutList,
mutThreshRange=2:4, windowSizeRange=2:4)
dbMutList supplied; skipped calling calcObservedMutations()
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Analyzing combinations of windowSizeRange and mutThreshRange
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|=============================== | 44%>>> mutThresh = 3 > windowSize = 2 (skipped)
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|====================================================== | 78%>>> mutThresh = 4 > windowSize = 2 (skipped)
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$`2`
2 3 4
[1,] FALSE NA NA
[2,] FALSE NA NA
[3,] FALSE NA NA
[4,] FALSE NA NA
[5,] FALSE NA NA
$`3`
2 3 4
[1,] FALSE FALSE NA
[2,] FALSE FALSE NA
[3,] TRUE FALSE NA
[4,] TRUE FALSE NA
[5,] FALSE FALSE NA
$`4`
2 3 4
[1,] TRUE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] TRUE FALSE FALSE
[4,] TRUE FALSE FALSE
[5,] FALSE FALSE FALSE
See also¶
slideWindowDb is called on db for tuning. See slideWindowTunePlot
for visualization. See calcObservedMutations for generating dbMutList.