CIMseqSwarm: CIMseqSwarm

In EngeLab/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Description

Subtitle

Usage

## S4 method for signature 'CIMseqSwarm'
getData(x, n = NULL)

## S4 method for signature 'CIMseqSwarm'
c(x, ...)

## S4 method for signature 'CIMseqSwarm'
filterSwarm(x, subset)

CIMseqSwarm(singlets, multiplets, ...)

## S4 method for signature 'CIMseqSinglets,CIMseqMultiplets'
CIMseqSwarm(
  singlets,
  multiplets,
  useMuSiC = FALSE,
  maxiter = 10,
  swarmsize = 150,
  nSyntheticMultiplets = 200,
  seed = 11,
  norm = TRUE,
  report = FALSE,
  reportRate = NA,
  vectorize = FALSE,
  permute = FALSE,
  singletIdx = NULL,
  cacheScores = FALSE,
  psoControl = list(),
  startSwarm = NULL,
  topK = NULL,
  multiplet.factor = NA,
  ...
)

## S4 method for signature 'CIMseqSwarm'
initialize(
  .Object,
  ...,
  fractions,
  costs,
  convergence,
  stats,
  singletIdx,
  arguments
)

## S4 method for signature 'CIMseqSwarm'
show(object)

Arguments

x	CIMseqSwarm; A CIMseqSwarm object.
n	character; Data to extract from CIMseqSwarm object.
...	additional arguments to pass on.
subset	Indicates samples to be retained. Can be a character vector of sample names, a logical vector, or integer vector indicating sample indices.
singlets	CIMseqSinglets; A CIMseqSinglets object.
multiplets	CIMseqMultiplets; A CIMseqMultiplets object.
maxiter	integer; The maximum optimization iterations.
swarmsize	integer; The number of swarm particals.
nSyntheticMultiplets	Numeric; Value indicating the number of synthetic multiplets to generate during deconvolution.
seed	integer; Seed to set before running.
norm	logical; Indicates if the sum of fractions should equal 1.
report	logical; Indicates if additional reporting from the optimization should be included.
reportRate	integer; If report is TRUE, the iteration interval for which a report should be generated.
vectorize	logical, Argument to psoptim.
permute	logical; indicates if genes should be permuted before deconvolution. For use with permutation testing. @param singletIdx list; Singlet indexes to be used to choose singlets and synthesize synthetic multiplets. Facilitates using the same synthetic set e.g. with repeated runs or permutation.
singletIdx	list; Indexes indicating singlets that were subset to synthesize synthetic multiplets. Facilitates recreation of the synthetic multiplets downstream.
cacheScores	logical; Use score caching optimization (experimental) Requires R package hashmap to be installed
.Object	Internal object.
fractions	matrix; The deconvolution results.
costs	numeric; The costs after optimization.
convergence	character; The convergence output from psoptim. One value per multiplet.
stats	tbl_df; The stats output from psoptim
arguments	list; Arguments passed to the CIMseqSwarm function.
object	CIMseqSwarm; A CIMseqSwarm to show.
swarmPos	matrix; Final swarm positions from psoptim

Details

Description

Value

CIMseqSwarm output.

Author(s)

Jason T. Serviss

Examples

#use demo data

EngeLab/CIMseq documentation built on Jan. 25, 2022, 5 a.m.