Description Usage Arguments Value Author(s) See Also Examples
These functions provide tools to investigate the permutation distribution of test statistics, raw (unadjusted) p-values, and class labels.
1 2 3 | mt.sample.teststat(V,classlabel,test="t",fixed.seed.sampling="y",B=10000,na=.mt.naNUM,nonpara="n")
mt.sample.rawp(V,classlabel,test="t",side="abs",fixed.seed.sampling="y",B=10000,na=.mt.naNUM,nonpara="n")
mt.sample.label(classlabel,test="t",fixed.seed.sampling="y",B=10000)
|
V |
A numeric vector containing the data for one of the variables (genes). |
classlabel |
A vector of integers corresponding to observation (column)
class labels. For k classes, the labels must be integers
between 0 and k-1. For the |
test |
A character string specifying the statistic to be
used to test the null hypothesis of no association between the
variables and the class labels. |
side |
A character string specifying the type of rejection region. |
fixed.seed.sampling |
If |
B |
The number of permutations. For a complete
enumeration, |
na |
Code for missing values (the default is |
nonpara |
If |
For mt.sample.teststat
, a vector containing B
permutation test statistics.
For mt.sample.rawp
, a vector containing B
permutation unadjusted p-values.
For mt.sample.label
, a matrix containing B
sets of permuted class labels. Each row corresponds to one permutation.
Yongchao Ge, yongchao.ge@mssm.edu,
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Gene expression data from Golub et al. (1999)
data(golub)
mt.sample.label(golub.cl,B=10)
permt<-mt.sample.teststat(golub[1,],golub.cl,B=1000)
qqnorm(permt)
qqline(permt)
permt<-mt.sample.teststat(golub[50,],golub.cl,B=1000)
qqnorm(permt)
qqline(permt)
permp<-mt.sample.rawp(golub[1,],golub.cl,B=1000)
hist(permp)
|
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