getTPs: Gets the number of true positives in the top n counts...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/getTPs.R

Description

If the true positives are known, this function will return a vector, the ith member of which gives the number of true positives identified if the top i counts, based on estimated posterior likelihoods, are chosen.

Usage

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getTPs(cD, group, decreasing = TRUE, TPs)

Arguments

cD

countData object, containing posterior likelihoods for each group.

group

Which group should we give the counts for? See Details.

decreasing

Ordering on posterior likelihoods.

TPs

Known true positives.

Details

In the rare (or simulated) cases where the true positives are known, this function will calculate the number of true positives selected at any cutoff.

The 'group' can be defined either as the number of the element in '[email protected]' or as a string which will be partially matched to the names of the '[email protected]' elements.If group = NULL, then the function looks at the posterior likelihoods that the data have no true differential expression (if calculated).

Value

A vector, the ith member of which gives the number of true positives identified if the top i counts are chosen.

Author(s)

Thomas J. Hardcastle

See Also

countData

Examples

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# See vignette for more examples.

# We load in a `countData' object containing the estimated posterior
# likelihoods of expression (see `getLikelihoods').

data(CDPost)

# If the first hundred rows in the 'simData' matrix are known to be
# truly differentially expressed (the second hypothesis defined in the
# 'groups' list) then we find the number of true positives for the top n
# genes selected as the nth member of

getTPs(CDPost, group = "DE", decreasing = TRUE, TPs = 1:100)

baySeq documentation built on Nov. 17, 2017, 12:06 p.m.