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

Description Usage Arguments Value Examples

View source: R/functions.R

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

1
2
3
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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 March 29, 2018, 1:23 p.m.