R/SpectralTAD_Par.R
SpectralTAD_Par.RdParallelized 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
)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.
Vector of chromosomes in the same order as their corresponding contact matrices. Must be same length as cont_list. Required.
The number of levels of the TAD hierarchy to be calculated. The default setting is 1.
Option to turn on quality filtering which removes TADs with negative silhouette scores (poorly organized TADs). Default is FALSE.
Option to filter sub-TADs based on the z-score of their eigenvector gaps. Default is TRUE.
The number of eigenvectors to be calculated. The default and suggested setting is 2.
The minimum allowable TAD size measured in bins. Default is 5.
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
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.
Parameter to determine whether the result should be a GRangeList object. Defaults to FALSE
Corresponds to the percentage of zeros allowed before a column/row is removed from analysis. 1=100%, .7 = 70%, etc. Default is 1.
Number of cores to use. Defaults to total available cores minus one.
Vector of labels used to name each contact matrix. Must be same length as cont_list. Default is NULL.
List of lists where each entry is a list of data frames or GRanges in BED format corresponding to TADs seperated by hierarchies
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.
#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, cores = 2)
#> Converting to n x n matrix
#> Matrix dimensions: 2517x2517
#> Estimating resolution
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Converting to n x n matrix
#> Matrix dimensions: 2517x2517
#> Estimating resolution
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.
#> Warning: Unknown or uninitialised column: `Group`.