Description Creating objects Slots Methods Author(s) See Also Examples

This is the class representation for the results of a tail-rank test to find biomarkers in a microarray data set. It includes methods for summarizing and plotting the results of the test.

Although objects can be created, as usual, using `new`

, the only
reliable way to create valid objects is to use the
`TailRankTest`

function. See the description of that
function for details on how the tail-rank test works.

`statistic`

:a numeric vector containng the tail-rank statistic for each row (gene) in a microarray data set

`direction`

:a character string representing the direction of the test; can be "up", "down", or "two-sided"

`N1`

:an integer; the numnber of samples in the "base" or "healthy" group

`N2`

:an integer; the number of samples in the "test" or "cancer" group

`specificity`

:a real number between 0 and 1; the desired specificity used in the test to estimate a quantile from the "base" group

`tolerance`

:a real number between 0 and 1; the upper tolerance bound used to estimate the threshold

`confidence`

:a real number between 0 and 1; the confidence level that there are no false positives

`cutoff`

:an integer; the maximum expected value of the statistic under the null hypothesis

`model`

:a character string describing the model (binomial or beta-binomial) used to decide on cutoffs for significance

`tau`

:a numeric vector or NULL; gene-by-gene upper bounds for significance

`rho`

:a numeric vector or NULL; gene-by-gene lower bounds for significance

- summary(object, ...)
Display a summary of the TailRankTest

`object`

- hist(x, overlay, ...)
Plot a histogram of the statistic in the TailRankTest object

`x`

. The optional argument`overlay`

is a logical flag. If`overlay=TRUE`

, then the histogram is overlain with a curve representing the null distribution. The default value of`overlay`

is`FALSE`

.- as.logical(x, ...)
Convert the TailRankTest object

`x`

into a logical vector, which takes on a`TRUE`

value whenever the tail-rank statistic exceeds the significance cutoff.- getStatistic(object, ...)
Obtain the vector of tail-rank statistics contained in

`object`

.

Kevin R. Coombes <krc@silicovore.com>

`TailRankTest`

,
`tailRankPower`

,
`biomarkerPowerTable`

,
`matrixMean`

,
`toleranceBound`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
# generate some fake data to use in the example
nr <- 40000
nc <- 110
fake.data <- matrix(rnorm(nr*nc), ncol=nc)
fake.class <- rep(c(TRUE, FALSE), c(40, 70))
# perform the tail-rank test
null.tr <- TailRankTest(fake.data, fake.class)
# get a summary of the results
summary(null.tr)
# plot a histogram of the statistics
hist(null.tr, overlay=TRUE)
# get the actual statistics
stats <- getStatistic(null.tr)
# get a vector that selects the "positive" calls for the test
is.marker <- as.logical(null.tr)
# the following line should evaluate to the number of rows, nr = 40000
sum( is.marker == (stats > null.tr@cutoff) )
``` |

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