COTAN_ObjectCreation: 'COTAN' shortcuts

In seriph78/COTAN: COexpression Tables ANalysis

COTAN shortcuts

Description

These functions create a COTAN object and/or also run all the necessary steps until the genes' COEX matrix is calculated.

Usage

COTAN(raw = "ANY")

## S4 method for signature 'COTAN'
proceedToCoex(
  objCOTAN,
  calcCoex = TRUE,
  optimizeForSpeed = TRUE,
  deviceStr = "cuda",
  cores = 1L,
  cellsCutoff = 0.003,
  genesCutoff = 0.002,
  cellsThreshold = 0.99,
  genesThreshold = 0.99,
  saveObj = TRUE,
  outDir = "."
)

automaticCOTANObjectCreation(
  raw,
  GEO,
  sequencingMethod,
  sampleCondition,
  calcCoex = TRUE,
  optimizeForSpeed = TRUE,
  deviceStr = "cuda",
  cores = 1L,
  cellsCutoff = 0.003,
  genesCutoff = 0.002,
  cellsThreshold = 0.99,
  genesThreshold = 0.99,
  saveObj = TRUE,
  outDir = "."
)

Arguments

raw	a matrix or dataframe with the raw counts
objCOTAN	a newly created COTAN object
calcCoex	a Boolean to determine whether to calculate the genes' COEX or stop just before at the estimateDispersionBisection() step
optimizeForSpeed	Boolean; when TRUE COTAN tries to use the torch library to run the matrix calculations. Otherwise, or when the library is not available will run the slower legacy code
deviceStr	On the torch library enforces which device to use to run the calculations. Possible values are "cpu" to us the system CPU, "cuda" to use the system GPUs or something like "cuda:0" to restrict to a specific device
cores	number of cores to use. Default is 1.
cellsCutoff	clean() will delete from the raw data any gene that is expressed in less cells than threshold times the total number of cells. Default cutoff is 0.003 \; (0.3\%)
genesCutoff	clean() will delete from the raw data any cell that is expressing less genes than threshold times the total number of genes. Default cutoff is 0.002 \; (0.2\%)
cellsThreshold	any gene that is expressed in more cells than threshold times the total number of cells will be marked as fully-expressed. Default threshold is 0.99 \; (99.0\%)
genesThreshold	any cell that is expressing more genes than threshold times the total number of genes will be marked as fully-expressing. Default threshold is 0.99 \; (99.0\%)
saveObj	Boolean flag; when TRUE saves intermediate analyses and plots to file
outDir	an existing directory for the analysis output.
GEO	a code reporting the GEO identification or other specific dataset code
sequencingMethod	a string reporting the method used for the sequencing
sampleCondition	a string reporting the specific sample condition or time point.

Details

Constructor of the class COTAN

proceedToCoex() takes a newly created COTAN object (or the result of a call to dropGenesCells()) and runs calculateCoex()

automaticCOTANObjectCreation() takes a raw dataset, creates and initializes a COTAN object and runs proceedToCoex()

Value

a COTAN object

proceedToCoex() returns the updated COTAN object with genes' COEX calculated. If asked to, it will also store the object, along all relevant clean-plots, in the output directory.

automaticCOTANObjectCreation() returns the new COTAN object with genes' COEX calculated. When asked, it will also store the object, along all relevant clean-plots, in the output directory.

Examples

data("test.dataset")
obj <- COTAN(raw = test.dataset)

#
# In case one needs to run more steps to clean the datatset
# the following might apply
if (FALSE) {
  objCOTAN <- initializeMetaDataset(objCOTAN,
                                    GEO = "test",
                                    sequencingMethod = "artificial",
                                    sampleCondition = "test dataset")
#
# doing all the cleaning...
#
# in case the genes' `COEX` is not needed it can be skipped
# (e.g. when calling [cellsUniformClustering()])
  objCOTAN <- proceedToCoex(objCOTAN, calcCoex = FALSE,
                            cores = 6L, optimizeForSpeed = TRUE,
                            deviceStr = "cuda", saveObj = FALSE)
}


## Otherwise it is possible to run all at once.
objCOTAN <- automaticCOTANObjectCreation(
  raw = test.dataset,
  GEO = "code",
  sequencingMethod = "10X",
  sampleCondition = "mouse_dataset",
  calcCoex = TRUE,
  saveObj = FALSE,
  outDir = tempdir(),
  cores = 6L)

seriph78/COTAN documentation built on Dec. 10, 2024, 3:30 a.m.