Description Usage Format Methods
A class to perform expression based 'spectrometry'.
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ExpSpect
class generator
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.
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