MAMA (version 2.1.0)

MAP.Matches: Wrapper function for MAP-Matches method

Description

This is a wrapper function for MAP-Matches method.

Usage

MAP.Matches(data, varname, t.cutoff = "98.00%", multiple = TRUE, perm = c("both", "columns", "labels")[1], nperm = 1000, test = c("t", "t.equalvar")[1], sig.col, sig.cutoff = 0.05)

Arguments

data

Object of class MetaArray

varname

Character String - name of one column in clinical data matrices to be used as class labels

t.cutoff

Character String - quantile of T statistics to be selected, e.g. "95.00%" selects the top 5 percent of absolute values

multiple

Logical - when TRUE only paterrns with multiple '1' are used

perm

Character String - if "labels" only class labels are permuted for statistical analysis (empirical significance), if "columns" only genes in each dataset are selected randomly, if "both" both class labels and genes ar

nperm

Numeric - number of permutations

test

Character String - if "t" then unequal variance t-test is used, if "t.equalvar" equal variance t-test is used

sig.col

Character String - which p-value is used for selection of significant patterns. Possible values are: "p.col.strong", "p.col.weak", "p.lab.strong", "p.lab.weak" , "col" refers to column permutations, "lab

sig.cutoff

Numeric - p-value for selection of sigificant patterns

Value

• Object of class MAP.Matches.res containing
• tests
  Data.frame of test statistics
• bin.matrix
  Binary matrix from tests, 1 means the test statistics was higer than threshold
• sumarization
  Sumarization of bin.matrix: number of selected genes in each dataset, genes with at least one 1 in pattern, probability of observing strong or soft match in the data
• MAP
  Data frame describing observed patterns: number of strong n.strong and soft n.soft matches and number of genes involved n.sig
• stat.analysis
  Results of statistical analysis
• genes
  List of genes observed with each pattern

References

Yang, X., Bentink, S. and Spang, R. 2005, Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities, Biomedical Microdevices, Vol.7:3, pp. 247-251

Examples

data(ColonData)
MAP.Matches(ColonData, "satelite", nperm = 100, sig.col="p.lab.strong")