Makesense {geneplotter} | R Documentation |
'Makesense' takes either an ExpressionSet
object or a matrix
of gene expressions and will produce a smoothed positive and negative strands
for all chromosomes.
Makesense(expr, lib, ...)
expr |
Either an ExpressionSet or a matrix of
gene expressions with genes as rows and columns as samples. |
lib |
The name of the Bioconductor annotation data package that
will be used to provide mappings from probes to chromosomal
locations, such as hgu95av2.db or hgu133a.db . If
expr is an ExpressionSet , the argument defaults to the
annotation slot of the ExpressionSet . |
... |
Currently, the only optional argument is f , the
smoother span to be passed to 'lowess'. Its value should
be in the interval of (0,1). This gives the proportion of points in
the plot which influence the smooth at each value. Larger values
give more smoothness. The default value for this argument is 1/10. |
The expr
argument can either be of class ExpressionSet
or
matrix
, where the latter represents the matrix of gene
expressions.
If the expr
argument is an ExpressionSet
, the lib
argument will use the annotation
slot. Users can override this
behaviour and supply their own lib
argument if they wish. If
the ExpressionSet
has no value associated with the annotation
slot (which should not happen, but is possible) then the user must
supply the lib
argument manually or the function will throw an
error.
A list of 2 components:
ans2 |
a list , whose components correspond to samples
in the same order as appearing in the columns of
'expr'. Each component is also a list , named by chromosomes
"1"-"22", "X" and "Y". Each named component is again a list
with two elements named "posS" and "negS", corresponding to the
positive and negative strands of a chromosome, each of which is an object returned by 'lowess'. |
lib |
A string giving the name of the annotation data package to
use. Optional if expr is an ExpressionSet . |
Robert Gentleman and Xiaochun Li
library("hgu133a.db") data(expressionSet133a) esetobj <- Makesense(exprs(expressionSet133a), "hgu133a") esetobj2 <- Makesense(expressionSet133a[1:200, ])