pudms: DMS experiments analysis using PUlasso method

In RomeroLab/pudms: Positive-Unlabeled Learning for the Analysis of Deep Mutational Scanning Datasets

Description

DMS experiments analysis using PUlasso method

Usage

pudms(
  protein_dat,
  py1 = NULL,
  order = 1,
  refstate = NULL,
  verbose = T,
  nobs_thresh = 10,
  lambda = 0,
  nlambda = 10,
  pvalue = T,
  n_eff_prop = 1,
  intercept = F,
  maxit = 1000,
  eps = 0.001,
  inner_eps = 0.01,
  initial_coef = NULL,
  p.adjust.method = "BH",
  outfile = NULL,
  nCores = 1,
  exclude_gap = TRUE
)

Arguments

protein_dat	input data. A data table containing (sequence, labeled, unlabeled, seqId)
py1	a numeric value representing the prevalence of positives in the unlabeled data
order	an integer; 1= main effects, 2= main effects + pairwise effects
refstate	a character which will be used for the common reference state; the default is to use the most frequent amino acid as the reference state for each of the position.
verbose	a logical value. The default is TRUE
nobs_thresh	the number of minimum required mutations per position
lambda	l1 penalty
nlambda	if lambda= NULL, a sequence of nlambda is created for fitting
pvalue	a logial value; if TRUE, p-values based on the asymptotic distribution are obtained
n_eff_prop	proportion of an effective sample size
intercept	a logical value; if TRUE, an estimated intercept is reported together with other coefficients
maxit	maximum number of iterations
eps	convergence threshold for the outer loop
inner_eps	convergence threshold for the inner loop
initial_coef	a vector representing an initial point where we start PUlasso algorithm from.
p.adjust.method	method for multiple comparison
outfile	NULL or a string; if a string is provided, an output with the name of the string will be exported in a working directory.
nCores	the number of threads for computing.
exclude_gap	a logical value. The default is TRUE. If TRUE, mutations corresponding to the gap (*) will not be considered for group p-value calculations

Value

a list containing a fit (from grpPUlasso), result_table (data.frame), and refstate

RomeroLab/pudms documentation built on Jan. 2, 2021, 5:10 a.m.