ROCplot
(Package: leapp) :
plot ROC curve
Input an p by d matrix, each column of which contains false positive rates(FPR) computed from each of the d methods and p significance levels and a matrix of corresponding true positive rates(TPR) at the same significance levels. Plot ROC curve for each of the d methods.
● Data Source:
CranContrib
● Keywords: misc
● Alias: ROCplot
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Given a vector of sizes of retrieved genes, for each size k, select the top k genes with smallest p values and compute the recall from the retrieved genes and the true positive genes.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: FindRec
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FindPrec
(Package: leapp) :
compute the precision at given sizes of retrieved genes
Given a vector of sizes of retrieved genes, for each size k, select the top k genes with smallest p values and compute the precision from the retrieved genes and the true positive genes.
● Data Source:
CranContrib
● Keywords: misc
● Alias: FindPrec
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leapp
(Package: leapp) :
latent effect adjustment after primary projection
Adjust for latent factors and conduct multiple hypotheses testing from gene expression data using the algorithm of Sun,Zhang and Owen (2011). Number of latent factors can be chosen by Buja and Eyuboglu (1992).
● Data Source:
CranContrib
● Keywords: misc
● Alias: leapp
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ridge
(Package: leapp) :
Outlier detection with a ridge penalty
Outlier detection and robust regression with a ridge type penalty on the outlier indicator gamma. Allow non sparse outliers and require known noise standard deviation.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: ridge
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Outlier detection and robust regression through an iterative penalized regression with tuning parameter chosen by modified BIC
● Data Source:
CranContrib
● Keywords: ipod, ~kwd2
● Alias: IPOD
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Y = X beta + gamma + sigma epsilon estimate k by 1 coefficients vector beta and N by 1 outlier indicator vector gamma from (Y,X).
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: IPODFUN
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FindTpr
(Package: leapp) :
compute the true positive rate at given sizes of retrieved genes
Given a vector of sizes of retrieved genes, for each size k, select the top k genes with smallest p values and compute the true positive rate from the retrieved genes and the true positive genes.
● Data Source:
CranContrib
● Keywords: misc
● Alias: FindTpr
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Pvalue
(Package: leapp) :
Calculate statistics and p-values
Calculate F-statistics, t-statistics and corresponding p-values given multiple regression models under the null and alternative hypotheses.
● Data Source:
CranContrib
● Keywords: misc
● Alias: Pvalue
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These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
● Data Source:
CranContrib
● Keywords: package
● Alias: leapp-package
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providing 
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