samr.pvalues.from.perms: Report estimated p-values for each gene, from a SAM analysis

In samr: SAM: Significance Analysis of Microarrays

Description

Report estimated p-values for each gene, from set of permutations in a SAM analysis

Usage

samr.pvalues.from.perms(tt, ttstar)

Arguments

tt	Vector of gene scores, returned by samr in component tt
ttstar	Matrix of gene scores (p by nperm) from nperm permutations. Returned by samr in component ttstar

Author(s)

Jun Li and Balasubrimanian Narasimhan and Robert Tibshirani

References

Taylor, J. and Tibshirani, R. (2005): A tail strength measure for assessing the overall significance in a dataset. Submitted.

Examples

#generate some example data
set.seed(100)
x<-matrix(rnorm(1000*20),ncol=20)
dd<-sample(1:1000,size=100)

u<-matrix(2*rnorm(100),ncol=10,nrow=100)
x[dd,11:20]<-x[dd,11:20]+u

y<-c(rep(1,10),rep(2,10))

data=list(x=x,y=y, geneid=as.character(1:nrow(x)),
genenames=paste("g",as.character(1:nrow(x)),sep=""), logged2=TRUE)
samr.obj<-samr(data,  resp.type="Two class unpaired", nperms=100)

pv=samr.pvalues.from.perms(samr.obj$tt, samr.obj$ttstar)

Example output

Loading required package: impute
Loading required package: matrixStats
perm= 1
perm= 2
perm= 3
perm= 4
perm= 5
perm= 6
perm= 7
perm= 8
perm= 9
perm= 10
perm= 11
perm= 12
perm= 13
perm= 14
perm= 15
perm= 16
perm= 17
perm= 18
perm= 19
perm= 20
perm= 21
perm= 22
perm= 23
perm= 24
perm= 25
perm= 26
perm= 27
perm= 28
perm= 29
perm= 30
perm= 31
perm= 32
perm= 33
perm= 34
perm= 35
perm= 36
perm= 37
perm= 38
perm= 39
perm= 40
perm= 41
perm= 42
perm= 43
perm= 44
perm= 45
perm= 46
perm= 47
perm= 48
perm= 49
perm= 50
perm= 51
perm= 52
perm= 53
perm= 54
perm= 55
perm= 56
perm= 57
perm= 58
perm= 59
perm= 60
perm= 61
perm= 62
perm= 63
perm= 64
perm= 65
perm= 66
perm= 67
perm= 68
perm= 69
perm= 70
perm= 71
perm= 72
perm= 73
perm= 74
perm= 75
perm= 76
perm= 77
perm= 78
perm= 79
perm= 80
perm= 81
perm= 82
perm= 83
perm= 84
perm= 85
perm= 86
perm= 87
perm= 88
perm= 89
perm= 90
perm= 91
perm= 92
perm= 93
perm= 94
perm= 95
perm= 96
perm= 97
perm= 98
perm= 99
perm= 100

samr documentation built on May 1, 2019, 7:49 p.m.