Description Usage Arguments Details Value Author(s) See Also Examples
Takes posterior likelihoods and returns the counts with highest (or lowest) likelihood of association with a given group.
1 2 
cD 

group 
Which group should we give the counts for? See Details. 
ordering 
If specified, restricts the analysis to a particlar ordering on the group. 
decreasing 
Ordering on posterior likelihoods. 
number 
How many results should be returned? 
likelihood 
If given, ignores ‘number’ and returns all results above a certain likelihood (and FDR, and FWER, if given). 
FDR 
If given, ignores ‘number’ and returns all results with an FDR lower than this threshold (and likelihood, and FWER, if given). 
FWER 
If given, ignores ‘number’ and returns all results with an FWER lower than this threshold (and likelihood, and FDR, if given). 
normaliseData 
Should the displayed counts be normalised? See details. Defaults to FALSE. 
posteriors 
If given, a vector of logposterior likelihoods to use instead of those in the ‘@posteriors’ slot of the ‘cD’ object. 
The argument 'group' can be specified either as a number, giving the
index of an element in the [email protected]
list, or as a character
string identifying an element by name. Partial matching is allowed. If
group = NULL, then the function looks at the posterior likelihoods
that the data have no true differential expression (if calculated).
If a countData
object is given, the returned dataframe
will contain either the raw counts for that object, or (if
'normaliseData = TRUE' the counts normalised by library size.
A dataframe of the top counts associated with some model (group), described by annotation drawn from the '@annotation' slot of the 'cD' object and the raw data from the '@data' slot, together with the posterior likelihoods and false discovery rates.
Thomas J. Hardcastle
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19  # We load in a `countData' object containing the estimated posterior
# likelihoods of expression (see `getLikelihoods').
data(CDPost)
# Report the top ten rows of data that have highest likelihood of belonging to
# group 2 of the data (i.e., differentially expressed)
topCounts(CDPost, group = "DE", number = 10)
# equivalently...
topCounts(CDPost, group = 2, number = 10)
# Report the top ten rows of data that have highest likelihood of belonging to
# group 2 of the data (i.e., differentially expressed), with group 1
# being overexpressed compared to group 2.
topCounts(CDPost, group = "DE", ordering = "1>2", number = 10)

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