genAFold {ABSSeq} | R Documentation |
Calculate aFold for each gene and general sd
genAFold(nncounts, cond, preval = 0.05, qforkappa = 0, pair = FALSE, priorgenesd)
nncounts |
matrix for read count. |
cond |
factor for conditions. If provide only one condition, fold-change estimation will be suppressed. |
preval |
pre-defined scale control for variance normalization, default is 0.05, a large value generally increases the fold-changes (decreases penalty of variances) under low expression. |
qforkappa |
quantile for estimating kappa(>=qforkappa), default is 0 (without trimming of data). Please set up a value in [0,1) if you want to trim the low expressed data. |
pair |
switch for paired samples, default is false |
priorgenesd |
prior value for general SD of fold change, if provided, the estimation of general SD will be replaced by this value. |
shifted and calculate a set of parameters from normalized counts table before callDEs
A list with log2 foldchange, general SD for calculating pvalue, variance stabilized counts and expression level adjusted counts (used for PCA analysis)
This function should run after normalFactors
.
data(simuN5) obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups)) mtx <- counts(obj,TRUE) aFold <- genAFold(mtx,factor(simuN5$groups)) hist(aFold[[1]])