findMotifHits scans sequences (either provided
as a file, an R object or genomic coordinates) for matches to
positional weight matrices (provided as a file or as R objects)
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for character,character
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for character,DNAString
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for character,DNAStringSet
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrix,character
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrix,DNAString
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrix,DNAStringSet
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrixList,character
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrixList,DNAString
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrixList,DNAStringSet
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrix,GRanges
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)
# S4 method for PWMatrixList,GRanges
findMotifHits(
query,
subject,
min.score,
method = c("matchPWM", "homer2"),
homerfile = findHomer("homer2"),
BPPARAM = SerialParam(),
genome = NULL
)The motifs to search for, either a
character(1) with the path and file name of a motif
file with PWM in HOMER format (currently only
supported for method="homer2")
PWMatrix with a single PWM
PWMatrixList with several PWMs to search for.
The sequences to be searched, either a
character with the path and file name of a sequence
file with DNA sequences in FASTA format
DNAString with a single sequence
DNAStringSet with several sequences
GRanges object with the genomic coordinates
of the sequences to be searched.
The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "85 highest possible score or as a single number.
The internal method to use for motif searching. One of
"matchPWM" using Biostrings::matchPWM (optimized)
"homer2" call to the homer2 binary
Please note that the two methods might give slightly different results (see details).
Path and file name of the homer2 binary.
An optional BiocParallelParam
instance determining the parallel back-end to be used during evaluation.
BSgenome object that is the reference genome of the
subject. This argument is set to NULL by default and only used by the
function when the subject is a GRanges object. It is then
necessary to specify the genome so that the function can internally
convert the genomic regions into a DNAStringSet object.
A GRanges object with the matches to query in
subject.
The implemented methods (matchPWM and homer2) are
there for convenience (method="matchPWM" calls
Biostrings::matchPWM internally in an optimized fashion, and
method = "homer2" calls the command line tool from Homer and
therefore requires an installation of Homer).
In general, running findMotifHits with the same parameters using
any of the methods generates identical results. Some minor differences
could occur that result from rounding errors during the necessary
conversion of PWMs (log2-odd scores) to the probability matrices needed
by Homer, and the conversion of scores from and to the natural log scale
used by Homer. These conversions are implemented transparently for the
user, so that the arguments of findMotifHits do not have to be
adjusted (e.g. the PWMs should always contain log2-odd scores, and
min.score is always on the log2 scale).
If there are bases with frequencies of less than 0.001 in a motif, Homer
will set them to 0.001 and adjust the other frequencies at that motif
position accordingly so that they sum to 1.0. This may differ from the
adjustment used when scanning a PWM with matchPWM (e.g. the
pseudocounts argument in the toPWM
function), and thus can give rise to differences in reported motif hits
and hit scores (typically only low-scoring hits).
seqs <- Biostrings::DNAStringSet(c(s1 = "GTCAGTCGATC", s2 = "CAGTCTAGCTG",
s3 = "CGATCGTCAGT", s4 = "AGCTGCAGTCT"))
m <- rbind(A = c(2, 0, 0),
C = c(1, 1, 0),
G = c(0, 2, 0),
T = c(0, 0, 3))
pwms <- TFBSTools::PWMatrixList(
TFBSTools::PWMatrix(ID = "m1", profileMatrix = m),
TFBSTools::PWMatrix(ID = "m2", profileMatrix = m[, 3:1])
)
findMotifHits(pwms, seqs, min.score = 7)
#> GRanges object with 6 ranges and 4 metadata columns:
#> seqnames ranges strand | matchedSeq pwmid pwmname score
#> <Rle> <IRanges> <Rle> | <DNAStringSet> <Rle> <Rle> <numeric>
#> [1] s1 4-6 + | AGT m1 Unknown 7
#> [2] s1 2-4 - | TGA m2 Unknown 7
#> [3] s2 2-4 + | AGT m1 Unknown 7
#> [4] s3 9-11 + | AGT m1 Unknown 7
#> [5] s3 7-9 - | TGA m2 Unknown 7
#> [6] s4 7-9 + | AGT m1 Unknown 7
#> -------
#> seqinfo: 4 sequences from an unspecified genome