sleuth_object_result: Retrieve all results from a given Sleuth object following...

In nodrogluap/gumshoe: Supplemental Statistical Tests and Utilities for Kallisto/Sleuth RNASeq Analysis

Retrieve all results from a given Sleuth object following statistical testing

Description

Retrieve all results from a given Sleuth object following statistical testing

Usage

sleuth_object_result(
  sleuth_obj,
  all_data = FALSE,
  sig_data = TRUE,
  single_df = FALSE,
  retrived_from_model = FALSE,
  q_max = 0.05,
  test = "wt"
)

Arguments

sleuth_obj	An existing Sleuth object as generated by sleuth_prep() and fit by sleuth_fit()
all_data	A Boolean value that indicates whether all results of the Wald test should be assigned to a variable. Automatic assignment to a variable in the global environment. Defaults to FALSE
sig_data	A Boolean value that indicates whether all the significant results of the Wald test coupled with fdr_cutoff should be assigned to a variable. Automatic assignment to a variable in the global environment. Defaults to TRUE.
single_df	A Boolean value that indicates whether all the results of Wald test should be merged into a single data frame and returned. Returned data must be manually assigned to variable when calling with single_df = TRUE. Defaults to FALSE.
retrived_from_model	A Boolean value that indicates whether the data frame returned should include an additional column that includes the model that the data is from. This parameter is unique to single_df as both all_data and sig_data automatically assign data to variables in the global environment. Defaults to FALSE.
q_max	The FDR cutoff value that is passed to the fdr_cutoff function embedded within sleuth_object_result. Defaults to .05.
test	The sleuth test to be analyzed using sleuth_results, can be either "wt" or "lrt". Defaults to "wt".

Value

Either automatically generated variables (all_data and sig_data) containing resulting data from the Wald or Likewise Ratio tests with or without an FDR cutoff applied or all test result data in a manually assigned single data frame

Examples

# Given a Sleuth object and Boolean values of tests to run, perform the requested tests on all possible models for the given Sleuth object
sleuth_object_result(so, q_max = .01, test = "lrt")

nodrogluap/gumshoe documentation built on Feb. 28, 2023, 6:15 p.m.