A script that performs many RUV analyses, generates plots, tables, etc., and nicely formats the output in an html file. This script is useful for getting a quick first look at your data; it should not be considered to provide a final or complete analysis. More information about the usage of this script is provided in the how-to file in the "inst" sub-directory of the ruv.extras package.
ruv_starter_analysis(Y, X, ctl, Z = 1, eta = NULL, pctl = NULL, genecoloring = NULL, samplecoloring = NULL, genetexts = NULL, sampletexts = NULL, genesymbols = NULL, samplesymbols = NULL, geneinfo = NULL, rankbybeta = FALSE, topN = 40, topcount_thresholds = c(20, 40, 60, 80, 100), rankset = NULL, kset = c(1, 2, 3, 5, 7, 10, 15, 20, 30, 50, 75, 100, 200, 500, 1000, 2000, 5000, 10000), factorset = 1:5, bin = 10, do_general = TRUE, do_unadjusted = TRUE, do_ruv2 = TRUE, do_ruv4 = TRUE, do_ruvinv = TRUE, do_ruvrinv = TRUE, do_pptable = TRUE, outdir = "html", initialize_collapsed = FALSE, webtitle = "RUV Starter Analysis", inputcheck = TRUE, verbose = FALSE)
Y |
The data. A m by n matrix, where m is the number of samples and n is the number of features. |
X |
The factor of interest. A m by 1 matrix, where m is the number of samples. |
ctl |
The negative controls. A logical vector of length n. |
Z |
Any additional covariates to include in the model. Either a m by q matrix of covariates, or simply 1 (the default) for an intercept term. |
eta |
Gene-wise (as oposed to sample-wise) covariates. These covariates are adjusted for by RUV-1 before any further analysis proceeds. A matrix with n columns. |
pctl |
Positive controls. A logical vector of length n. |
genecoloring |
A vector of length n. The colors to use when plotting genes. |
samplecoloring |
A vector of length m. The colors to use when plotting samples. |
genetexts |
A vector of length n. Any text to be used in place of symbols, when plotting genes. Elements that are NA are plotted as symbols. |
sampletexts |
A vector of length m. Any text to be used in place of symbols, when plotting samples. Elements that are NA are plotted as symbols. |
genesymbols |
A vector of length n. The plot symbols to use when plotting genes. |
samplesymbols |
A vector of length m. The plot symbols to use when plotting symbols. |
geneinfo |
A matrix with n rows. Each column should contain some information about the genes (such as their names) for use in tables. |
rankbybeta |
Should the analysis include a ranking of the features based on the absolue value of estimated effect size (betahat)? |
topN |
The number of top-ranked genes to include in tables. |
topcount_thresholds |
The thresholds to use when counting the number of top-ranked positive controls. |
rankset |
The genes to be considered when determining which are top-ranked. A logical vector. NULL implies all genes. |
kset |
Which values of K should be considered. |
factorset |
Which factors should be included in the projection plot table. |
bin |
The bin size in the method of empirical variances. |
do_general |
Should the "general" analysis be performed? |
do_unadjusted |
Should the "unadjusted" analysis be performed? |
do_ruv2 |
Should the RUV-2 analysis be performed? |
do_ruv4 |
Should the RUV-4 analysis be performed? |
do_ruvinv |
Should the RUV-inv analysis be performed? |
do_ruvrinv |
Should the RUV-rinv analysis be performed? |
do_pptable |
Should the factor projection plot table be created? |
outdir |
Directory where the web page should be written. |
initialize_collapsed |
Should the web page be created so that only headers are shown, and must be manually expanded? |
webtitle |
The title of the web page. |
inputcheck |
Perform a basic sanity check on the inputs, and issue a warning if there is a problem. |
verbose |
Verbose output. |
Does not return a (meaningful) value. Generates a web page.