evaluateK: Evaluate the optimal number of knots required for fitGAM.

In tradeSeq: trajectory-based differential expression analysis for sequencing data

Description

Evaluate the optimal number of knots required for fitGAM.

Evaluate an appropriate number of knots.

Usage

evaluateK(counts, ...)

## S4 method for signature 'matrix'
evaluateK(
  counts,
  k = 3:10,
  nGenes = 500,
  sds = NULL,
  pseudotime = NULL,
  cellWeights = NULL,
  U = NULL,
  conditions = NULL,
  plot = TRUE,
  weights = NULL,
  offset = NULL,
  aicDiff = 2,
  verbose = TRUE,
  parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(),
  control = mgcv::gam.control(),
  family = "nb",
  gcv = FALSE,
  ...
)

## S4 method for signature 'dgCMatrix'
evaluateK(
  counts,
  k = 3:10,
  nGenes = 500,
  sds = NULL,
  pseudotime = NULL,
  cellWeights = NULL,
  plot = TRUE,
  U = NULL,
  weights = NULL,
  offset = NULL,
  aicDiff = 2,
  verbose = TRUE,
  conditions = NULL,
  control = mgcv::gam.control(),
  parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(),
  family = "nb",
  gcv = FALSE,
  ...
)

## S4 method for signature 'SingleCellExperiment'
evaluateK(
  counts,
  k = 3:10,
  nGenes = 500,
  sds = NULL,
  pseudotime = NULL,
  cellWeights = NULL,
  plot = TRUE,
  U = NULL,
  weights = NULL,
  offset = NULL,
  aicDiff = 2,
  verbose = TRUE,
  conditions = NULL,
  parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(),
  control = mgcv::gam.control(),
  family = "nb",
  gcv = FALSE,
  ...
)

## S4 method for signature 'CellDataSet'
evaluateK(
  counts,
  k = 3:10,
  nGenes = 500,
  sds = NULL,
  pseudotime = NULL,
  cellWeights = NULL,
  plot = TRUE,
  U = NULL,
  weights = NULL,
  offset = NULL,
  aicDiff = 2,
  verbose = TRUE,
  conditions = NULL,
  parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(),
  control = mgcv::gam.control(),
  family = "nb",
  gcv = FALSE,
  ...
)

Arguments

counts	The count matrix, genes in rows and cells in columns.
...	parameters including:
k	The range of knots to evaluate. '3:10' by default. See details.
nGenes	The number of genes to use in the evaluation. Genes will be randomly selected. 500 by default.
sds	Slingshot object containing the lineages.
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.
conditions	This argument is in beta phase and should be used carefully. If each lineage consists of multiple conditions, this argument can be used to specify the conditions. tradeSeq will then fit a condition-specific smoother for every lineage.
plot	Whether to display diagnostic plots. Default to TRUE.
weights	Optional: a matrix of weights with identical dimensions as the counts matrix. Usually a matrix of zero-inflation weights.
offset	Optional: the offset, on log-scale. If NULL, TMM is used to account for differences in sequencing depth, see fitGAM.
aicDiff	Used for selecting genes with significantly varying AIC values over the range of evaluated knots to make the barplot output. Default is set to 2, meaning that only genes whose AIC range is larger than 2 will be used to check for the optimal number of knots through the barplot visualization that is part of the output of this function.
verbose	logical, should progress be verbose?
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	Control object for GAM fitting, see mgcv::gam.control().
family	The distribution assumed, currently only "nb" (negative binomial) is supported.
gcv	(In development). Logical, should a GCV score also be returned?

Details

The number of parameter to evaluate (and therefore the runtime) scales in k * the number of lineages. Morevoer, we have found that, in practice, values of k above 12-15 rarely lead to improved result, not matter the complexity of the trajectory being considered. As such, we recommand that user proceed with care when setting k to value higher than 15.

Value

A plot of average AIC value over the range of selected knots, and a matrix of AIC and GCV values for the selected genes (rows) and the range of knots (columns).

Examples

## This is an artifical example, please check the vignette for a realistic one.
set.seed(8)
data(sds, package="tradeSeq")
loadings <- matrix(runif(2000*2, -2, 2), nrow = 2, ncol = 2000)
counts <- round(abs(t(slingshot::reducedDim(sds) %*% loadings))) + 100
aicK <- evaluateK(counts = counts, sds = sds, nGenes = 100,
                  k = 3:5, verbose = FALSE)

tradeSeq documentation built on Nov. 8, 2020, 7:51 p.m.