Function which takes the output of
assembles the connections into a data frame with cicero co-accessibility
A list of cicero output objects, generally, the
Logical, should the function run silently?
This function combines glasso models computed on overlapping windows of the genome. Pairs of sites whose regularized correlation was calculated twice are first checked for qualitative concordance (both zero, positive or negative). If they not concordant, NA is returned. If they are concordant the mean is returned.
A data frame of connections with their cicero co-accessibility scores.
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data("cicero_data") data("human.hg19.genome") sample_genome <- subset(human.hg19.genome, V1 == "chr18") sample_genome$V2 <- 100000 input_cds <- make_atac_cds(cicero_data, binarize = TRUE) input_cds <- reduceDimension(input_cds, max_components = 2, num_dim=6, reduction_method = 'tSNE', norm_method = "none") tsne_coords <- t(reducedDimA(input_cds)) row.names(tsne_coords) <- row.names(pData(input_cds)) cicero_cds <- make_cicero_cds(input_cds, reduced_coordinates = tsne_coords) model_output <- generate_cicero_models(cicero_cds, distance_parameter = 0.3, genomic_coords = sample_genome) cicero_cons <- assemble_connections(model_output)
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