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Screen sequences for positions with PWM scores meeting a threshold condition

screen_local_pwm.Rd

This function screens sequences to find positions where the local PWM score meets a specified threshold condition using various operators (>, <, >=, <=, ==).

Usage

screen_local_pwm(
  sequences,
  pssm,
  operator,
  threshold,
  spat = NULL,
  spat_min = 0,
  spat_max = NULL,
  bidirect = TRUE,
  prior = 0.01
)

Arguments

sequences

a vector of sequences

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').

operator

A character string specifying the comparison operator. One of: ">", "<", ">=", "<=", "=="

threshold

A numeric value specifying the threshold for comparison

spat

a data frame with the spatial model (as returned from the $spat slot 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.

Value

A list with one element per sequence, where each element is a numeric vector containing the 1-indexed positions that meet the threshold condition.

Examples

if (FALSE) { # \dontrun{
# Find positions where HNF1A motif scores above -19
hnf1a_positions <- screen_local_pwm(
    cluster_sequences_example,
    as.matrix(MOTIF_DB["JASPAR.HNF1A"]),
    operator = ">",
    threshold = -37
)

which(purrr::map_dbl(hnf1a_positions, length) > 0) # which sequences have positions?
hnf1a_positions[[4]] # positions for the 4th sequence

hnf1a_energy <- compute_local_pwm(cluster_sequences_example, as.matrix(MOTIF_DB["JASPAR.HNF1A"]))
hnf1a_energy[4, hnf1a_positions[[4]]]
} # }