Package 'metagenomeSeq' - Bioconductor

fitMeta 17fitMetaComputes a slightly modified form of Metastats.DescriptionUsageWrapper to perform the permutation test on the t-statistic. This is the original method employedby metastats (for non-sparse large samples). We include CSS normalization though (optional) andlog2 transform the data. In this method the null distribution is not assumed to be a t-dist.fitMeta(obj, mod, useCSSoffset = TRUE, B = 1000, coef = 2, sl = 1000)ArgumentsobjmoduseCSSoffsetBcoefslA MRexperiment object with count data.The model for the count distribution.Boolean, whether to include the default scaling parameters in the model or not.Number of permutations.The coefficient of interest.The value to scale by (default=1000).ValueCall made, fit object from lmFit, t-statistics and p-values for each feature.fitPAWrapper to run fisher’s test on presence/absence of a feature.DescriptionUsageThis function returns a data frame of p-values, odds ratios, lower and upper confidence limits forevery row of a matrix.fitPA(obj, cl, thres = 0)ArgumentsobjclthresA MRexperiment object with a count matrix, or a simple count matrix.Group comparisonThreshold for defining presence/absence.