fitGAM {tradeSeq}R Documentation

fitGAM

Description

This fits the NB-GAM model as described in Van den Berge et al.[2019]

Usage

fitGAM(counts, ...)

## S4 method for signature 'matrix'
fitGAM(counts, sds = NULL, pseudotime = NULL,
  cellWeights = NULL, U = NULL, weights = NULL, offset = NULL,
  nknots = 6, verbose = TRUE, parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(), control = mgcv::gam.control(),
  sce = FALSE, family = "nb")

Arguments

counts

the count matrix.

...

parameters including:

sds

an object of class SlingshotDataSet, typically obtained after running Slingshot. If this is provided, pseudotime and cellWeights arguments are derived from this object.

pseudotime

a matrix of pseudotime values, each row represents a cell and each column represents a lineage.

cellWeights

a matrix of cell weights defining the probability that a cell belongs to a particular lineage. Each row represents a cell and each column represents a lineage.

U

the design matrix of fixed effects. The design matrix should not contain an intercept to ensure identifiability.

weights

a matrix of weights with identical dimensions as the counts matrix. Usually a matrix of zero-inflation weights.

offset

the offset, on log-scale. If NULL, TMM is used to account for differences in sequencing depth., see edgeR::calcNormFactors. Alternatively, this may also be a matrix of the same dimensions as the expression matrix.

nknots

Number of knots used to fit the GAM. Defaults to 6.

verbose

Logical, should progress be printed?

parallel

Logical, defaults to FALSE. Set to TRUE if you want to parallellize the fitting.

BPPARAM

object of class bpparamClass that specifies the back-end to be used for computations. See bpparam in BiocParallel package for details.

control

Variables to control fitting of the GAM, see gam.control.

sce

Should output be of SingleCellExperiment class? This argument should not be changed by users.

family

The assumed distribution for the response, set to "nb" by default.

Value

A list of length the number of genes (number of rows of counts). Each element of the list is either a gamObject if the fiting procedure converged, or an error message.

Examples

set.seed(8)
data(crv, package="tradeSeq")
data(countMatrix, package="tradeSeq")
gamList <- fitGAM(counts = as.matrix(countMatrix),
                  sds = crv,
                  nknots = 5)

[Package tradeSeq version 1.0.1 Index]