Description Usage Arguments Value Author(s) See Also Examples

Runs a quick association analysis on the dataset against a phenotype/categorical variable stored in a dataframe, and uses the results as a way to select a subset of the original matrix, so you may wish to select the 'N' least associated variables, or the 'N' most associated.

1 2 | ```
select.least.assoc(bigMat, keep = 0.05, phenotype = NULL, least = TRUE,
dir = "", n.cores = 1, verbose = TRUE)
``` |

`bigMat` |
a big.matrix object, or any argument accepted by get.big.matrix(), which includes paths to description files or even a standard matrix object. |

`keep` |
numeric, by default a proportion (decimal) of the original number of rows/columns to choose for the subset. Otherwise if an integer>2 then will assume this is the size of the desired subset, e.g, for a dataset with 10,000 rows where you want a subset size of 1,000 you could set 'keep' as either 0.1 or 1000. |

`phenotype` |
a vector which contains the categorical variable to perform an association test for phenotype, etc. This should be the same length as the number of columns (e.g, samples) in bigMat. |

`least` |
logical, whether to select TRUE, the top least associated variables, or FALSE, the most associated. |

`dir` |
directory containing the filebacked.big.matrix, same as dir for get.big.matrix. |

`n.cores` |
integer, if wanting to process the analysis using multiple cores, specify the number |

`verbose` |
logical, whether to display additional output |

A set of row or column indexes (depents on 'rows' parameter) of the variables most dependent (or indepent) variables measured by association with a [continuous/categorical] phenotype.

Nicholas Cooper

1 2 3 4 5 6 | ```
bmat <- generate.test.matrix(5,big.matrix=TRUE)
pheno <- rep(1,ncol(bmat)); pheno[which(runif(ncol(bmat))<.5)] <- 2
most.correl <- select.least.assoc(bmat,phenotype=pheno,least=FALSE)
least.correl <- select.least.assoc(bmat,phenotype=pheno,least=TRUE)
cor(bmat[least.correl,][1,],pheno) # least correlated
cor(bmat[most.correl,][1,],pheno) # most correlated
``` |

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