summary-ZlmFit-method: Summarize model features from a 'ZlmFit' object

Description Usage Arguments Value See Also Examples

Description

Returns a data.table with a special print method that shows the top 2 most significant genes by contrast. This data.table contains columns:

primerid

the gene

component

C=continuous, D=discrete, logFC=log fold change, S=combined using Stouffer's method, H=combined using hurdle method

contrast

the coefficient/contrast of interest

ci.hi

upper bound of confidence interval

ci.lo

lower bound of confidence interval

coef

point estimate

z

z score (coefficient divided by standard error of coefficient)

Pr(>Chisq)

likelihood ratio test p-value (only if doLRT=TRUE)

Some of these columns will contain NAs if they are not applicable for a particular component or contrast.

Usage

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## S4 method for signature 'ZlmFit'
summary(object, logFC = TRUE, doLRT = FALSE,
  level = 0.95, ...)

Arguments

object

A ZlmFit object

logFC

If TRUE, calculate log-fold changes, or output from a call to getLogFC.

doLRT

if TRUE, calculate lrTests on each coefficient, or a character vector of such coefficients to consider.

level

what level of confidence coefficient to return. Defaults to 95 percent.

...

ignored

Value

data.table

See Also

print.summaryZlmFit

Examples

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data(vbetaFA)
z <- zlm(~Stim.Condition, vbetaFA[1:5,])
zs <- summary(z)
names(zs)
print(zs)
##Select `datatable` copmonent to get normal print method
zs$datatable

MAST documentation built on Nov. 17, 2017, 1:28 p.m.