RGSEAsd {RGSEA} | R Documentation |
This is the function for classification with features from top and bottom deviating from the mean value of the whole transcriptome for a certain standard deviations of the subtset features.
RGSEAsd(query, reference, queryclasses, refclasses, random = 5000, sd = 2, iteration = 100)
query |
A matrix, The query data. This is the data which the research wants to know the class. |
reference |
A matrix. The reference data. Based of the reference data, the research infer the class of query data. |
queryclasses |
A character vector. It contains the classes of query data. If you don't know the classes of query data, just give it a character vector equal to the number of query data. |
refclasses |
A character vector. It contains the classes of reference data. You must know it. |
random |
A numeric variable. The number of features in the subset randomly sampled from the whole features each time. |
sd |
number of standard deviations the features selected from the subset deviate from the mean value of the subset. |
iteration |
A numeric varialbe. The times of random sampling. |
[1] The times of each sample in the reference dataset is the most similar to the query data. [2] The frequencey of features selected from the top and bottom of the subsets from the query data, if the query data is correcly classified.
Chengcheng Ma
if(interactive()) { data(cmap) test <- RGSEAsd(cmap[,1],cmap[,2:6], queryclasses=colnames(cmap)[1], refclasses=colnames(cmap)[2:6], random=5000, sd=2, iteration=100) }