getsLA-methods {LiquidAssociation} | R Documentation |
'getsLA' is used to calculate the sLA test statistic and correponding p value.
object |
An numerical matrix object with three columns or an object of ExpresionSet class with three features. |
boots |
The number of bootstrap iterations for estimating the bootstrap standard error of sGLA. Default value is boots=30. |
perm |
The number of permutation iterations for generating the null distribution of the sGLA test statistic. Default is perm=100. |
dim |
An index of the column for the gene to be treated as the third controller variable. Default is dim=3 |
geneMap |
A character vector with three elements representing the mapping between gene names and feature names (optional). |
The input object can be a numerical matrix with three columns with row representing observations and column representing three variables. It can also be an ExpressionSet object with three features. If input a matrix class data, all three columns of the object representing the variables should have column names. Each variable in the object will be standardized with mean 0 and variance 1 in the function. In addition, the third variable will be quantile normalized within the function. More detail example about the usage of geneMap is demonstrated in the vignette.
'getsLA' returns a vector with two elements. The first element is the value of test statistic and second element is the corresponding p value. A more detailed interpretation of these values is illustrated in the vignette.
LA, getsGLA
data<-matrix(rnorm(300), ncol=3) colnames(data)<-c("Gene1", "Gene2", "Gene3") sLAest<-getsLA(data, boots=20, perm=100) sLAest