SingleFeatureMatrix: SingleFeatureMatrix
In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

SingleFeatureMatrix

R Documentation

SingleFeatureMatrix

Run FeatureMatrix on a single Fragment object

SingleFeatureMatrix(
  fragment,
  features,
  cells = NULL,
  process_n = 2000,
  sep = c("-", "-"),
  verbose = TRUE
)

`fragment`	A list of `Fragment` objects. Note that if setting the `cells` parameter, the requested cells should be present in the supplied `Fragment` objects. However, if the cells information in the fragment object is not set (`Cells(fragments)` is `NULL`), then the fragment object will still be searched.
`features`	A GRanges object containing a set of genomic intervals. These will form the rows of the matrix, with each entry recording the number of unique reads falling in the genomic region for each cell.
`cells`	Vector of cells to include. If NULL, include all cells found in the fragments file
`process_n`	Number of regions to load into memory at a time, per thread. Processing more regions at once can be faster but uses more memory.
`sep`	Vector of separators to use for genomic string. First element is used to separate chromosome and coordinates, second separator is used to separate start and end coordinates.
`verbose`	Display messages