iResViewer: Interactive visualization of differential gene expression...

In csoneson/iResViewer: Interactive visualization of differential expression results

Description

Interactive visualization of differential gene expression results

Usage

iResViewer(wideResults = list(), longResults = list(), dimReds = list(),
  geneModels = NULL, geneInfo = NULL, bwFiles = NULL, bwCond = NULL,
  abundances = list(), appTitle = "iResViewer", ...)

Arguments

wideResults	Named list of result data frames. These will be displayed as searchable tables, each in its own tab.
longResults	Named list of result data frames in "long" form (one row per gene/contrast combination). These will be used to generate volcano plots. Each data frame should have at least four columns: gene (the gene ID), logFC (log-fold change), FDR (adjusted p-value) and mlog10PValue (-log10(nominal p-value)).
dimReds	Named list of dimension reduction results. Each element of the list must have at least three columns: two columns with coordinates in the low-dimensional space and one column with sample IDs or group labels.
geneModels	A GRanges object with gene models, typically generated from a gtf file.
geneInfo	Data frame with gene annotation information. Should have at least two columns: gene (the gene ID) and symbol (the gene symbol).
bwFiles	Named vector with paths to bigWig files. These will be used to generate coverage plots.
bwCond	Named vector corresponding to bwFiles, giving the group label for each bigWig file. These will be used to color the coverage plots by group.
abundances	Named list with data frames in "long" format (one row per gene/sample combination), containing abundance estimates. These will be used to illustrate the abundance pattern for selected genes. Each data frame must have at least four columns: sample (the sample ID), gene (the gene ID), value (the abundance) and group (a sample group label, used to order and color the points in the plot).
appTitle	App title
...	Additional arguments (currently not used)

Author(s)

Charlotte Soneson

csoneson/iResViewer documentation built on May 28, 2019, 7:49 p.m.