Description Usage Arguments Value Examples
View source: R/momentum_routines.R
Structure-based gene velocity estimation
1 2 3 4 5 6 7 8 | global.velcoity.estimates(emat, nmat, vel, base.df, deltaT = 1,
smat = NULL, kGenes = 15, kGenes.trim = 5, smooth.kGenes = 0,
kCells = 10, deltaT2 = 1, min.gene.conuts = 100,
min.gene.cells = 20, min.intron.length = 10^3.5,
min.exon.length = 10^2.7, top.global.pearson.deviance = 3,
cellKNN = NULL, cell.dist = NULL, fit.quantile = NULL,
zero.offset = NULL, diagonal.quantiles = FALSE, m.pcount = 5,
plot.model.fit = FALSE, n.cores = defaultNCores())
|
emat |
- spliced (exonic) count matrix |
nmat |
- unspliced (nascent) count matrix |
vel |
- initial gene-relative velocity estimates (output of the gene.relative.velocity.estimates function) |
base.df |
gene structure information data frame ($gene.df in output of read.gene.mapping.info()), containing the following columns ($il - total intronic length in log10(length+1) scale; $el - total exonic length; $nex - number of expressed (above some low threshold) exons; as well as optional $nipconc/$nipdisc giving number of concordant and discordant internal priming sites) |
deltaT |
- amount of time to project the cell forward |
smat |
- optional spanning read matrix (used in offset calculations) |
kGenes |
- number of genes to use in evaluating trimmed mean of M values |
kGenes.trim |
- number of genes to trim (from both ends) |
smooth.kGenes |
- gene kNN pooling k value (used in the initial gene-relative fit) |
kCells |
- number of k nearest neighbors (NN) to use in slope calculation smoothing |
deltaT2 |
- scaling of the projected difference vector (normally should be set to 1) |
min.gene.conuts |
- minimum number of spliced reads/molecules that a gene should have |
min.gene.cells |
- minimum number of cells in which a gene should be expressed |
min.intron.length |
- minimum exon length |
min.exon.length |
- minimum exon length |
top.global.pearson.deviance |
- maximum deviance threshold to filter out genes with very high unsplied counts (likely due to other processes) |
cellKNN |
- optional pre-calculated cell KNN matrix |
cell.dist |
- cell distance to use in cell kNN pooling calculations |
fit.quantile |
perform gamma fit on a top/bottom quantiles of expression magnitudes |
zero.offset |
force gene offsets to be zero (default if smat is not supplied), otherwise estimated from the lower quantile or quantile fit |
diagonal.quantiles |
whether diagonal quantile determination should be used (if fit.quantile is specified) |
m.pcount |
- pseudocount to be used in M value calculations (defaults to 5) |
plot.model.fit |
plot gamma values predicted by the structure-bsaed model as a function of gene-relative gamma estimates. |
n.cores |
- number of cores to use |
a list with velocity results, including the current normalized expression state ($current), projected ($projected), unscaled transcriptional change ($deltaE), fit results ($ko, $sfit), optional cell pooling parameters ($cellKNN, $kCells), kNN-convolved normalized matrices (conv.nmat.norm and conv.emat.norm)
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
# emat / nmat are the spliced/unpsliced matrices respectively
# rvel is a gene-relative velocity estimate
# base.df (here dat$base.df) is a gene information table.
# For SMART-seq2, it is part of the \code{\link{read.smartseq2.bams}} output.
# For droplet data, this info can be obtained \code{\link{}}
gvel <- global.velcoity.estimates(emat, nmat, rvel, dat$base.df, deltaT=1, kCells=5,
kGenes = 15, kGenes.trim = 5, min.gene.cells = 0, min.gene.conuts = 500)
## End(Not run)
|
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