logisticModel: Accessibility residuals from unconstrained quasibinomial...

In plantformatics/Socrates: Analysis of scATAC-seq data

Accessibility residuals from unconstrained quasibinomial logistic regression

Description

Run unregularized logistic regression. Output is unconstrained Pearson's residuals for each cell and ACR.

Usage

logisticModel(
  obj,
  r.variates = "~log10nSites",
  variates = NULL,
  nthreads = 1,
  chunks = 256,
  type = "pearson",
  link = "logit",
  center.resid = TRUE,
  scale.resid = FALSE,
  make.sparse = FALSE,
  verbose = FALSE,
  slotName = "residuals"
)

Arguments

obj	list containing a slot named 'counts' for the dgCMatrix object with binary cell (columns) x peak (rows) accessibility scores, and a slot named 'meta' containing a data.frame with barcode meta data information.
r.variates	model formula specifying variable to regress out. Should be specified as a character string. Defaults to "~log10nSites". Changing this parameter is not recommended.
variates	model formula as character string to regress out variables from the initial residuals using QR residuals in a second round of regression. Ideal for specifying batch effects, cell-cycle and other technical sources of variation. Defaults to NULL.
nthreads	numeric, number of threads to run logistic model in parallel. Depends on doSNOW. Defaults to 1.
chunks	numeric, number of peaks to run for each daughter process. Defaults to 256.
type	character, specify the residual type to extract from the model. Defaults to "pearson".
link	character, specify the link-function type for logistic regression. Possible parameters are "logit" and "probit". Defaults to "logit".
center.resid	logical, whether to zero-center residuals. Defaults to TRUE.
scale.resid	logical, whther to standardize residuals. Defaults to FALSE.
make.sparse	logical, whether or not to set negative values to 0, and reduce memory usage. Setting this parameter to TRUE has negligible effects on downstream results. Setting make.sparse to TRUE will override center.resid and scale.resid arguments, setting them to FALSE. Defaults to FALSE.
verbose	logical. Defaults to FALSE.
slotName	character, specify the slot name for saving residuals. Useful for saving multiple normalization steps. Note, make sure to update the slotName argument for downstream functions. Defaults to "residuals".

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.