summary,ZlmFit-method {MAST} | R Documentation |
ZlmFit
objectReturns a data.table
with a special print method that shows the top 2 most significant genes by contrast.
This data.table
contains columns:
the gene
C=continuous, D=discrete, logFC=log fold change, S=combined using Stouffer's method, H=combined using hurdle method
the coefficient/contrast of interest
upper bound of confidence interval
lower bound of confidence interval
point estimate
z score (coefficient divided by standard error of coefficient)
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.
## S4 method for signature 'ZlmFit' summary(object, logFC = TRUE, doLRT = FALSE, level = 0.95, ...)
object |
A |
logFC |
If TRUE, calculate log-fold changes, or output from a call to |
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 |
data.table
print.summaryZlmFit
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