get_fcs: get_fcs

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

Description

Functional class scoring

Usage

get_fcs(target.data, target.data.annot = NA, kegg_species_code = "hsa", 
database = c("pathway","module","brite","lipidmaps_mainclass","lipidmaps_subclass",
"refmet_superclass","refmet_mainclass","refmet_subclass","reactome_compound",
"reactome_atlas","kegg_atlas","custom"),
reference_set = NA, type.statistic = "pvalue", fcs.min.hits = 2, itrs = 100, numnodes = 2)

Arguments

target.data	Data frame with variable ID in column A and the statistic (eg. pvalue, t-statistic, fold change, VIP) in column B
target.data.annot	Optional argument with annotation data for the variables in target.data
kegg_species_code	KEGG species code if using KEGG as the reference database (e.g. hsa)
database	Options include: c("pathway","module","brite","lipidmaps_mainclass", "lipidmaps_subclass", "refmet_superclass","refmet_mainclass", "refmet_subclass","reactome_compound", "reactome_atlas","kegg_atlas","custom") The reactome_atlas and kegg_atlas options include all genes, compounds, and proteins associated with each pathway in the databases.
reference_set	If cutom database option is selected, then a data frame with the reference database should be provided with the functional class/pathway ID in column A, variable ID (e.g. compound name/ID) in column B, and set/pathway name in column C
type.statistic	Type of test statistic (e.g. pvalue, t-statistic,fold change)
fcs.min.hits	Minimum number of hits in a functional class (e.g. 2)
itrs	Number of permutations to generate the null distribution (e.g. 100)
numnodes	Number of CPUs to use (e.g. 2)

Details

The algorithm uses the z-statistic method proposed by Irizarry et al.(2009) and the max-mean method proposed by Efron and Tibshirani (2006) for determining significance of each functional class. The p-values from the two methods are aggregated using the Chi-square method.

Value

A data frame with aggregated statistic, p-value

Author(s)

Karan Uppal

kuppal2/xmsPANDA documentation built on May 15, 2021, 5:48 a.m.