Calculate the frequency of a position weight matrix (PWM) in a given set of intervals
gextract.local_pwm_freq.RdCalculate the frequency of a position weight matrix (PWM) in a given set of intervals
Usage
gextract.local_pwm_freq(
intervals,
pssm,
q_threshold,
bg_intervals = NULL,
spat = NULL,
spat_min = 0,
spat_max = NULL,
bidirect = TRUE,
prior = 0.01,
n_sequences = 10000,
dist_from_edge = 3000000,
chromosomes = NULL
)Arguments
- intervals
The intervals to extract
- pssm
a PSSM matrix or data frame. The columns of the matrix or data frame should be named with the nucleotides ('A', 'C', 'G' and 'T').
- q_threshold
The quantile threshold of the PWM (e.g. 0.99 for the top percentile)
- bg_intervals
(optional) an intervals set for the background. If not provided, random intervals will be used
- spat
a data frame with the spatial model (as returned from the
$spatslot from the regression). Should contain a column called 'bin' and a column called 'spat_factor'.- spat_min
the minimum position to use from the sequences. The default is 1.
- spat_max
the maximum position to use from the sequences. The default is the length of the sequences.
- bidirect
is the motif bi-directional. If TRUE, the reverse-complement of the motif will be used as well.
- prior
a prior probability for each nucleotide.
- n_sequences
number of sequences to sample in order to compute the quantiles. The default is 1e4.
- dist_from_edge
The minimum distance from the edge of the chromosome for a region to start or end(default: 3e6)
- chromosomes
The chromosomes to sample from (default: all chromosomes)