Create an McTracks object — mct

Create an McTracks object either from a list of tracks (tracks parameter) or from a track prefix (track_prefix parameter). The tracks are assumed to be in the form of ".+_mcmetacell_number", if this is not the case, the metacells parameter can be used to specify the metacell number for each track.

Usage

mct_create(
  genome,
  tracks = NULL,
  track_prefix = NULL,
  metacells = NULL,
  marginal_track = NULL,
  id = NULL,
  description = NULL,
  path = NULL,
  metadata = NULL,
  resolution = NULL,
  window_size = resolution/2,
  order = NULL
)

Arguments

genome: genome assembly of the tracks. e.g. "hg38", "hg19", "mm9", "mm10"
tracks: a vector of tracks to include in the object.
track_prefix: prefix for tracks (instead of explicit track names at the tracks parameter). Ignored if tracks is not NULL. If a track named "track_prefix.marginal" exists, it will be used as the marginal track.
metacells: a vector of metacells to include in the object (optional). If not provided, the metacells are inferred from the track names using the pattern "track_prefix.mc\d*$". In such a case, the tracks are ordered according to the metacell number.
marginal_track: a track to use as the marginal track (optional). If not provided, and track_prefix was given, the track named "track_prefix.marginal" will be used if it exists.
id: an identifier for the object, e.g. "pbmc".
description: description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)"
path: path to a directory containing the raw data. Usually inherited from the counts object.
metadata: data frame with a column called 'metacell' and additional metacell annotations, or the name of a delimited file which contains such annotations.
resolution: the resolution of the tracks.
window_size: The size of the window used to smooth the counts in each track. If no smoothing was done - this should be equal to resolution / 2.
order: the order of the tracks in the object. If not provided, the tracks are ordered according to the metacell number.

Value

a McTracks object.

Examples

if (FALSE) {
mct_create(track_prefix = "pbmc_mc", genome = "hg38", id = "pbmc", description = "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)")
}