ExpSpect: ExpSpect class

In JovingeLabSoftware/ExpSpect: Calculate protein specific biases in gene expression

Description

A class to perform expression based 'spectrometry'.

Usage

exps = ExpSpect$new()

Format

ExpSpect class generator

Methods

calcScores(data, treated, untreated, sigs, method=c('ks', 'excos'), normalize=TRUE, ...)

Given a gene expression matrix data, computes fold change based on columns given in vectors treated and untreated, and then computes enrichment scores against each column of matrix sigs. The sigs matrix is simply a matrix of gene expression data, one column per pertubagen which can be generated in any number of ways–assembled from GEO, downloaded from CMAP, extracted from LINCS, etc. See Vignette for an example. Data will be renormalized after fold change calculation prior to processing by method if normalize=TRUE. Extra-parameters (...) will be sent to selected function (see below for details)

cmap(data, y=NULL, up, down)

Given a gene expression matrix data, computes the connectivity score based on either a vector of expression data (y), or explicit sets of up and down regulated genes pertinent to a biological state or perturbation of interest. Returns the list of connectivity scores for each column of data. If providing a vector of expression values, up and down genes are s selected based on the provided threshold, after optional normalization (normalize = TRUE) step.

JovingeLabSoftware/ExpSpect documentation built on May 8, 2019, 4:38 p.m.