Compute the correlation between two given PSSMs

The correlation is computed by shifting the shorter PSSM along the longer one and computing the correlation at each position. The maximum correlation is returned.

Usage

pssm_cor(pssm1, pssm2, method = c("spearman", "pearson"), prior = 0.01)

Arguments

pssm1: first PSSM matrix or data frame
pssm2: second PSSM matrix or data frame
method: method to use for computing the correlation. See cor for details.
prior: a prior probability for each nucleotide.

Value

Correlation between the two PSSMs

Examples

if (FALSE) { # \dontrun{
res1 <- regress_pwm(cluster_sequences_example, cluster_mat_example[, 1])
pssm_cor(res1$pssm, JASPAR_motifs[JASPAR_motifs$motif == "HNF1A", ])
} # }

# Compare two motifs from MOTIF_DB
pssm_cor(as.matrix(MOTIF_DB["HOMER.GATA3_2"]), as.matrix(MOTIF_DB["JASPAR.CDX1"]))
#> [1] 0.3846587

# Compare using different correlation methods
pssm_cor(
    as.matrix(MOTIF_DB["HOMER.GATA3_2"]),
    as.matrix(MOTIF_DB["JASPAR.GATA3"]),
    method = "pearson"
)
#> [1] 0.2425705
pssm_cor(
    as.matrix(MOTIF_DB["HOMER.GATA3_2"]),
    as.matrix(MOTIF_DB["JASPAR.GATA3"]),
    method = "spearman"
)
#> [1] 0.3971397