Usage
stattest(gown = NULL, gowntable = NULL, pData = NULL, mod = NULL, mod0 = NULL, feature = c("gene", "exon", "intron", "transcript"), meas = c("cov", "FPKM", "rcount", "ucount", "mrcount", "mcov"), timecourse = FALSE, covariate = NULL, adjustvars = NULL, gexpr = NULL, df = 4, getFC = FALSE, libadjust = NULL, log = TRUE)
Arguments
gown
name of an object of class ballgown
gowntable
matrix or matrix-like object with rownames
representing feature IDs and columns representing samples, with expression
estimates in the cells. Provide the feature name with feature. You
must provide exactly one of gown or gowntable. NB: gowntable
is log-transformed within stattest if log is TRUE, so
provide un-logged expression values in gowntable.
pData
Required if gowntable is provided: data frame giving
phenotype data for the samples in the columns of gowntable. (Rows of
pData correspond to columns of gowntable). If gown is
used instead, it must have a non-null, valid pData slot (and the
pData argument to stattest should be left NULL).
mod
object of class model.matrix representing the design matrix
for the linear regression model including covariates of interest
mod0
object of class model.matrix representing the design
matrix for the linear regression model without the covariates of interest.
feature
the type of genomic feature to be tested for differential
expression. If gown is used, must be one of "gene",
"transcript", "exon", or "intron". If gowntable
is used, this is just used for labeling and can be whatever the rows of
gowntable represent.
meas
the expression measurement to use for statistical tests. Must be
one of "cov", "FPKM", "rcount", "ucount",
"mrcount", or "mcov". Not all expression measurements are
available for all features. Leave as default if gowntable is
provided.
timecourse
if TRUE, tests whether or not the expression
profiles of genomic features vary over time (or another continuous
covariate) in the study. Default FALSE. Natural splines are used
to fit time profiles, so you must have more timepoints than degrees of
freedom used to fit the splines. The default df is 4.
covariate
string representing the name of the covariate of interest
for the differential expression tests. Must correspond to the name of a
column of pData(gown). If timecourse=TRUE, this should be the
study's time variable.
adjustvars
optional vector of strings representing the names of
potential confounders. Must correspond to names of columns of
pData(gown).
gexpr
optional data frame that is the result of calling
gexpr(gown)). (You can speed this function up by pre-creating
gexpr(gown).)
df
degrees of freedom used for modeling expression over time with
natural cubic splines. Default 4. Only used if timecourse=TRUE.
getFC
if TRUE, also return estimated fold changes (adjusted for
library size and confounders) between populations. Only available for
2-group comparisons at the moment. Default FALSE.
libadjust
library-size adjustment to use in linear models. By default,
the adjustment is defined as the sum of the sample's log expression
measurements below the 75th percentile of those measurements. To use
a different library-size adjustment, provide a numeric vector of each
sample's adjustment value. Entries of this vector correspond to samples in
in rows of pData. If no library size adjustment is desired, set to
FALSE.
log
if TRUE, outcome variable in linear models is
log(expression+1), otherwise it's expression. Default TRUE.