scde.browse.diffexp: View differential expression results in a browser

In hms-dbmi/scde: Single Cell Differential Expression

View differential expression results in a browser

Description

Launches a browser app that shows the differential expression results, allowing to sort, filter, etc. The arguments generally correspond to the scde.expression.difference() call, except that the results of that call are also passed here. Requires Rook and rjson packages to be installed.

Usage

scde.browse.diffexp(results, models, counts, prior, groups = NULL,
  batch = NULL, geneLookupURL = NULL, server = NULL, name = "scde",
  port = NULL)

Arguments

results	result object returned by scde.expression.difference(). Note to browse group posterior levels, use return.posteriors = TRUE in the scde.expression.difference() call.
models	model matrix
counts	count matrix
prior	prior
groups	group information
batch	batch information
geneLookupURL	The URL that will be used to construct links to view more information on gene names. By default (if can't guess the organism) the links will forward to ENSEMBL site search, using geneLookupURL = "http://useast.ensembl.org/Multi/Search/Results?q = {0}". The "0" in the end will be substituted with the gene name. For instance, to link to GeneCards, use "http://www.genecards.org/cgi-bin/carddisp.pl?gene = {0}".
server	optional previously returned instance of the server, if want to reuse it.
name	app name (needs to be altered only if adding more than one app to the server using server parameter)
port	Interactive browser port

Value

server instance, on which $stop() function can be called to kill the process.

Examples

data(es.mef.small)
cd <- clean.counts(es.mef.small, min.lib.size=1000, min.reads = 1, min.detected = 1)
sg <- factor(gsub("(MEF|ESC).*", "\\1", colnames(cd)), levels = c("ESC", "MEF"))
names(sg) <- colnames(cd)

o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE)
o.prior <- scde.expression.prior(models = o.ifm, counts = cd, length.out = 400, show.plot = FALSE)
# make sure groups corresponds to the models (o.ifm)
groups <- factor(gsub("(MEF|ESC).*", "\\1", rownames(o.ifm)), levels = c("ESC", "MEF"))
names(groups) <- row.names(o.ifm)
ediff <- scde.expression.difference(o.ifm, cd, o.prior, groups = groups, n.randomizations = 100, n.cores = 10, verbose = 1)
scde.browse.diffexp(ediff, o.ifm, cd, o.prior, groups = groups, geneLookupURL="http://www.informatics.jax.org/searchtool/Search.do?query={0}")  # creates browser

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.