fastRUVIII: fastRUVIII

Description Usage Arguments Author(s)

View source: R/fastRUVIII.R

Description

perform fastRUVIII

Usage

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fastRUVIII(Y, M, ctl, k = NULL, eta = NULL, rsvd_prop = 0.1,
  include.intercept = TRUE, average = FALSE, fullalpha = NULL,
  return.info = FALSE, inputcheck = TRUE)

Arguments

Y

The unnormalised SC data. A m by n matrix, where m is the number of observations and n is the number of features.

M

The replicate mapping matrix. The mapping matrix has m rows (one for each observation), and each column represents a set of replicates. The (i, j)-th entry of the mapping matrix is 1 if the i-th observation is in replicate set j, and 0 otherwise. See ruv::RUVIII for more details.

ctl

An index vector to specify the negative controls. Either a logical vector of length n or a vector of integers.

k

The number of unwanted factors to remove. This is inherited from the ruvK argument from the scMerge::scMerge function.

eta

Gene-wise (as opposed to sample-wise) covariates. See ruv::RUVIII for details.

rsvd_prop

rsvd_prop is used to control for the accuracy of the randomized SVD computation. If a lower value is used on a lower dimensional data (say < 1000 cell) will potentially yield a less accurate computed result but with a gain in speed. The default of 0.1 tends to achieve a balance between speed and accuracy.

include.intercept

When eta is specified (not NULL) but does not already include an intercept term, this will automatically include one. See ruv::RUVIII for details.

average

Average replicates after adjustment. See ruv::RUVIII for details.

fullalpha

Not used. Please ignore. See ruv::RUVIII for details.

return.info

Additional information relating to the computation of normalised matrix. We recommend setting this to true.

inputcheck

We recommend setting this to true.

Author(s)

Yingxin Lin, John Ormerod, Kevin Wang


SydneyBioX/scMerge documentation built on Oct. 9, 2018, 3:28 p.m.