CIMseqConnections: CIMseqConnections

Description Usage Arguments Details Value Author(s) Examples

Description

Subtitle

Usage

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

CIMseqConnections(singlets, multiplets, swarm, ...)

## S4 method for signature 'CIMseqSinglets,CIMseqMultiplets,CIMseqSwarm'
CIMseqConnections(
  singlets,
  multiplets,
  swarm,
  alpha = 0.01,
  weightCut = 10,
  expectedWeightCut = 0,
  maxCellsPerMultiplet = 4,
  depleted = F,
  multiplet.factor = NA
)

Arguments

singlets

CIMseqSinglets; A CIMseqSinglets object.

multiplets

CIMseqMultiplets; A CIMseqMultiplets object.

swarm

CIMseqSwarm; A CIMseqSwarm object.

alpha

numeric; Vector of length 1 specifying the which p-values are considered significant.

weightCut

integer; Vector of length 1 specifying weights below which the p-value should not be calculated (set to non-zero for enrichment).

expectedWeightCut

integer; Vector of length 1 specifying expected weights below which the p-value should not be calculated (set to non-zero for depletion).

maxCellsPerMultiplet

integer; Vector of length 1 specifying the maximum size of a multiplet

depleted

logical; Set to TRUE to calculate depletion of connections rather than enrichment

multiplet.factor

numeric; Expected average size of multiplets. Used when ERCC controls are not provided. Should be estimated based on microscopy data. If it is not given, and no ERCC controls are provided, it will be estimated from the data (not recommended).

Details

Description

Value

CIMseqConnections output.

Author(s)

Martin Enge

Examples

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#use demo data

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