Compute correlation matrix for PSSM datasets

Usage

pssm_dataset_cor(
  dataset1,
  dataset2 = NULL,
  method = c("spearman", "pearson"),
  prior = 0.01
)

Arguments

dataset1: First PSSM dataset. A data frame with columns 'motif', 'A', 'C', 'G', 'T'
dataset2: Optional second PSSM dataset with the same structure as dataset1. If provided, computes correlations between motifs in dataset1 and dataset2. If NULL (default), computes correlations between all motifs in dataset1.
method: Method to use for correlation calculation ("spearman" or "pearson")
prior: A prior probability added to each nucleotide frequency (default: 0.01)

Value

If dataset2 is NULL, returns a symmetric square matrix of correlations between all motifs in dataset1. If dataset2 is provided, returns a matrix with rows corresponding to motifs in dataset1 and columns to motifs in dataset2.

Examples

if (FALSE) { # \dontrun{
# Correlations within a single dataset
cm <- pssm_dataset_cor(JASPAR_motifs)

# Correlations between two datasets
cm2 <- pssm_dataset_cor(JASPAR_motifs, HOMER_motifs)
} # }

# Correlations within MOTIF_DB (subset)
gata_motifs <- as.data.frame(MOTIF_DB["GATA", pattern = TRUE])
cm_gata <- pssm_dataset_cor(gata_motifs)

# Compare GATA motifs with CDX motifs
cdx_motifs <- as.data.frame(MOTIF_DB["CDX", pattern = TRUE])
cm_cross <- pssm_dataset_cor(gata_motifs, cdx_motifs)