SpectralTAD_Par: Parallelized Hierarchical Spectral Clustering of TADs
In SpectralTAD: SpectralTAD: Hierarchical TAD detection using spectral clustering

Description Usage Arguments Details Value Examples

View source: R/SpectralTAD_Par.R

Parallelized Hierarchical Spectral Clustering of TADs

SpectralTAD_Par(
  cont_list,
  chr,
  levels = 1,
  qual_filter = FALSE,
  z_clust = FALSE,
  eigenvalues = 2,
  min_size = 5,
  window_size = 25,
  resolution = "auto",
  grange = FALSE,
  gap_threshold = 1,
  cores = "auto",
  labels = NULL
)

`cont_list`	List of contact matrices where each is in either sparse 3 column, n x n or n x (n+3) form, where the first 3 columns are chromosome, start and end coordinates of the regions. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Required.
`chr`	Vector of chromosomes in the same order as their corresponding contact matrices. Must be same length as cont_list. Required.
`levels`	The number of levels of the TAD hierarchy to be calculated. The default setting is 1.
`qual_filter`	Option to turn on quality filtering which removes TADs with negative silhouette scores (poorly organized TADs). Default is FALSE.
`z_clust`	Option to filter sub-TADs based on the z-score of their eigenvector gaps. Default is TRUE.
`eigenvalues`	The number of eigenvectors to be calculated. The default and suggested setting is 2.
`min_size`	The minimum allowable TAD size measured in bins. Default is 5.
`window_size`	The size of the sliding window for calculating TADs. Smaller window sizes correspond to less noise from long-range contacts but limit the possible size of TADs
`resolution`	The resolution of the contact matrix. If none selected, the resolution is estimated by taking the most common distance between bins. For n x (n+3) contact matrices, this value is automatically calculated from the first 3 columns.
`grange`	Parameter to determine whether the result should be a GRangeList object. Defaults to FALSE
`gap_threshold`	Corresponds to the percentage of zeros allowed before a column/row is removed from analysis. 1=100%, .7 = 70%, etc. Default is 1.
`cores`	Number of cores to use. Defaults to total available cores minus one.
`labels`	Vector of labels used to name each contact matrix. Must be same length as cont_list. Default is NULL.

This is the parallelized version of the SpectralTAD() function. Given a sparse 3 column, an n x n contact matrix, or n x (n+3) contact matrix, SpectralTAD returns a list of TAD coordinates in BED format. SpectralTAD works by using a sliding window that moves along the diagonal of the contact matrix. By default we use the biologically relevant maximum TAD size of 2Mb and minimum size of 5 bins to determine the size of this window. Within each window, we calculate a Laplacian matrix and determine the location of TAD boundaries based on gaps between eigenvectors calculated from this matrix. The number of TADs in a given window is calculated by finding the number that maximize the silhouette score. A hierarchy of TADs is created by iteratively applying the function to sub-TADs. The number of levels in each hierarchy is determined by the user.

List of lists where each entry is a list of data frames or GRanges in BED format corresponding to TADs seperated by hierarchies

#Read in data
data("rao_chr20_25_rep")
#Make a list of matrices
mat_list = list(rao_chr20_25_rep, rao_chr20_25_rep)
#Make a vector of chromosomes
chr = c("chr20", "chr20")
#Make a vector of labels
labels = c("run1", "run2")
spec_table <- SpectralTAD_Par(mat_list, chr= chr, labels = labels)