Match PSSM to a directory of motifs — pssm

Match a PSSM to a directory of motifs. The PSSM is matched to each motif in the directory by computing the correlation between the two PSSMs.

Usage

pssm_match(
  pssm,
  motifs,
  best = FALSE,
  method = "spearman",
  parallel = getOption("prego.parallel", TRUE)
)

Arguments

pssm: PSSM matrix or data frame
motifs: a data frame with PSSMs ('A', 'C', 'G' and 'T' columns), with an additional column 'motif' containing the motif name
best: return the best match only
method: method to use for computing the correlation. See cor for details.
parallel: use parallel processing. Set the number of cores using set_parallel.

Value

if best is TRUE, a string with the best match. Otherwise, a data frame with a row per motif and a column named 'cor' with its correlation to pssm. The data frame is sorted by descreasing correlation.

Examples

if (FALSE) { # \dontrun{
res1 <- regress_pwm(cluster_sequences_example, cluster_mat_example[, 1])
head(pssm_match(res1$pssm, JASPAR_motifs))
pssm_match(res1$pssm, JASPAR_motifs, best = TRUE)
} # }