filter_data: Filter data according to thresholds.

In psmyth94/MetaProfiler: Metaproteomics Approach to Incorporation Profiling of Stable Isotopes

Description

Filter data according to thresholds.

Usage

filter_data(
  Object,
  peptide_centric = TRUE,
  LFDR_threshold = c("strong", "substantial"),
  min_nb_timepoints = 0,
  condition_names = colnames(Object@design)[colnames(Object@design) !=
    Object@time_unit],
  min_labeling_ratio = 0,
  min_nb_sample = NULL,
  score_threshold = NULL,
  higher_score_better = T,
  trace = T
)

Arguments

Object	An object of class MetaProfiler.
peptide_centric	Logical value specifying if filtering is done at the peptide or protein level. Protein level filtering is not yet fully implemented.
LFDR_threshold	Either a number or a character value "strong" or "substantial". If "strong" is chosen, then the threshold is 0.0909 (odds for false discoveries is 1 out of 10). If "substantial" is chosen, then the LFDR threshold is 0.2 (odds for false discovery is 1 out of 3).
min_nb_timepoints	Numeric value specifying the minimum number of timepoints the peptide or protein must be present in.
condition_names	A character vector specifying the conditions used in the experiment. Names must match the columns in Object@design. Defaults to all columns in Object@design, except for the column containing the timepoints. Names must match the columns in Object@design.
min_labeling_ratio	(Only used when estimate_prior_probability is set to "mle") A vector with two strings values. The first specifies the name of the distribution of RIA for true discoveries and the second specifies the distribution of LR for true discoveries. Can be either "weibull", "beta", "norm", "lnorm", "exp", "gamma", "invtrgamma", "trgamma", "lgamma", "pareto", "pareto1", "invweibull", "llogis", "invgamma", "unif", "cauchy", or "logis".
min_nb_sample	Numeric value specifying the minimum number of conditions the peptide or protein must be present in.
score_threshold	The score threshold.
higher_score_better	Logical value denoting if higher score is better.
trace	If TRUE, then progress is printed. Defaults to TRUE.

Value

Returns an object of class MetaProfiler.

Returns an object of class MetaProfiler.

Returns an object of class MetaProfiler.

psmyth94/MetaProfiler documentation built on Nov. 30, 2020, 1 p.m.