getPathwayStatistics {sigPathway} | R Documentation |
Gives the statistics for the probe sets associated with a pathway.
getPathwayStatistics(tab, phenotype, G, index, ngroups = 2, statList = NULL, keepUnknownProbes = FALSE)
tab |
a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively |
phenotype |
a numeric vector indicating the phenotype |
G |
a list containing the source, title, and probe sets associated with each curated pathway |
index |
an integer vector specifying the pathway(s) to summarize
in G |
ngroups |
an integer indicating the number of groups in the expression matrix |
statList |
a list containing results from calcTStatFast |
keepUnknownProbes |
a boolean indicating whether to keep the names of probe sets not represented in tab in the summary data frame |
This function gives the mean, standard deviation, and test statistic
for each in the pathway as indicated in G[[index]]
.
A data frame indicating the name, mean, standard deviation, the test
statistic (e.g., t-test), and the corresponding unadjusted p-value.
If ngroups
= 1, the Pearson correlation coefficient is also
returned.
See the help page for calculate.NTk
or calculate.NEk
for example code that uses getPathwayStatistics
Weil Lai