scRUVg {scMerge} | R Documentation |
Modified based on RUV2 from package ruv and RUVg from package RUVSeq function (see these function's documentations for full documentations and usage)
scRUVg(Y, ctl, k, Z = 1, eta = NULL, include.intercept = TRUE, fullW = NULL, svdyc = NULL)
Y |
The data. A m by n matrix, where m is the number of observations and n is the number of features. |
ctl |
index vector to specify the negative controls. |
k |
The number of unwanted factors to use. |
Z |
Any additional covariates to include in the model. |
eta |
Gene-wise (as opposed to sample-wise) covariates. |
include.intercept |
Applies to both Z and eta. When Z or eta (or both) is specified (not NULL) but does not already include an intercept term, this will automatically include one. If only one of Z or eta should include an intercept, this variable should be set to FALSE, and the intercept term should be included manually where desired. |
fullW |
Can be included to speed up execution. Is returned by previous calls of scRUVg |
svdyc |
Can be included to speed up execution. For internal use; please use fullW instead. |
A list consists of:
A matrix newY, the normalised matrix,
A matrix W, the unwanted variation matrix, and ;
A matrix alpha, this corresponding coefficient matrix for W.
Yingxin Lin, Kevin Wang
L = scMerge::ruvSimulate(m = 80, n = 1000, nc = 50, nCelltypes = 10) Y = L$Y; ctl = L$ctl ruvgRes = scMerge::scRUVg(Y = Y, ctl = ctl, k = 20)