Create a ChromatinAssay object from a count matrix or normalized data matrix. The expected format of the input matrix is features x cells. A set of genomic ranges must be supplied along with the matrix, with the length of the ranges equal to the number of rows in the matrix. If a set of genomic ranges are not supplied, they will be extracted from the row names of the matrix.

CreateChromatinAssay(
counts,
data,
min.cells = 0,
min.features = 0,
max.cells = NULL,
ranges = NULL,
motifs = NULL,
fragments = NULL,
genome = NULL,
annotation = NULL,
bias = NULL,
positionEnrichment = NULL,
sep = c("-", "-"),
validate.fragments = TRUE,
verbose = TRUE,
...
)

Arguments

counts Unnormalized data (raw counts) Normalized data; if provided, do not pass counts Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff. Include cells where at least this many features are detected. Include features detected in less than this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a higher cutoff. This can be useful for chromatin assays where certain artefactual loci accumulate reads in all cells. A percentage cutoff can also be set using 'q' followed by the percentage of cells, for example 'q90' will discard features detected in 90 percent of cells. If NULL (default), do not apply any maximum value. A set of GRanges corresponding to the rows of the input matrix A Motif object (not required) Path to a tabix-indexed fragments file for the data contained in the input matrix. If multiple fragment files are required, you can add additional Fragment object to the assay after it is created using the CreateFragmentObject and Fragments functions. Alternatively, a list of Fragment objects can be provided. A Seqinfo object containing basic information about the genome used. Alternatively, the name of a UCSC genome can be provided and the sequence information will be downloaded from UCSC. A set of GRanges containing annotations for the genome used A Tn5 integration bias matrix A named list of matrices containing positional signal enrichment information for each cell. Should be a cell x position matrix, centered on an element of interest (for example, TSS sites). Separators to use for strings encoding genomic coordinates. First element is used to separate the chromosome from the coordinates, second element is used to separate the start from end coordinate. Only used if ranges is NULL. Check that cells in the assay are present in the fragment file. Display messages Additional arguments passed to CreateFragmentObject