compute_statistically_relevant_phenotypes: Filter statistically relevant phenotypes by comparing two...

In SciOmicsLab/PhenoComb: Phenotype Combinatorial Analysis

Filter statistically relevant phenotypes by comparing two sample groups

Description

compute_statistically_relevant_phenotypes filters statistically relevant phenotypes by comparing two sample groups defined in sample_data.

Usage

compute_statistically_relevant_phenotypes(
  phenotype_cell_counts,
  channel_data,
  sample_data,
  test_type = "group",
  groups_column = NULL,
  g1 = NULL,
  g2 = NULL,
  correlation_column = NULL,
  survival_time_column = NULL,
  survival_status_column = NULL,
  max_pval = 0.05,
  parent_phen = NULL,
  n_threads = 1
)

Arguments

phenotype_cell_counts	Data.Frame object with marker and sample columns. Each row is a unique phenotype.
channel_data	Data.Frame containing columns named: Channel, Marker, T1, [T2, T3, ... , Tn], [OOB].
sample_data	Data.Frame containing a Sample_ID column and additional grouping columns for the samples.
test_type	Type of statistical test to be performed. Value can be "group", "correlation", or "survival". Default: "group". Additional parameters should be provided accordingly, such as [groups_column, g1, g2] for "group", [correlation_column] for "correlation", and [survival_time_column, survival_status_column] for "survival". Parameters not used in the test will be ignored.
groups_column	Column name in sample_data where group identifications are stored.
g1	Group label or vector with group labels for first group.
g2	Group label or vector with group labels for second group.
correlation_column	Column name in sample_data where data to be correlated is stored.
survival_time_column	Column name in sample_data where survival time is stored.
survival_status_column	Column name in sample_data where survival status is stored.
max_pval	Maximum p-value. Used to filter phenotypes in final output.
parent_phen	Parent phenotype to filter for. All phenotypes in the output will contain the parent phenotype.
n_threads	Number of threads to be used. Default: 1.

SciOmicsLab/PhenoComb documentation built on Aug. 26, 2023, 1:28 p.m.