OSCA_singleValue {modACDC} | R Documentation |
Function to return the percent variance explained in an external phenotype for a single dataset
OSCA_singleValue(
df,
externalVar,
oscaPath,
remlAlg = 0,
maxRemlIt = 100,
numCovars = NULL,
catCovars = NULL
)
df |
n x p dataframe or matrix of numeric -omics values with no ID column |
externalVar |
vector of length n of external variable values with no ID column |
oscaPath |
absolute path to OSCA software |
remlAlg |
which algorithm to run REML iterations in GCTA; 0 = average information (AI), 1 = Fisher-scoring, 2 = EM; default is 0 (AI) |
maxRemlIt |
the maximum number of REML iterations; default is 100 |
numCovars |
n x c_n matrix of numerical covariates to adjust heritability model for; must be in same person order as fam file; default is NULL |
catCovars |
n x c_c matrix of categorical covariates to adjust heritability model for; must be in same person order as fam file; default is NULL |
OmicS-data-based Complex trait Analysis (OSCA) is a suite of C++ functions. In order to use the OSCA functions, the user must specify the absolute path to the OSCA software, which can be downloaded from the Yang Lab website here.
Here, we use OSCA's Omics Restricted Maximum Likelihood (OREML) method to estimate the percent of variance in an external phenotype that can be explained by an omics profile, akin to heritability estimates in GWAS.
Row of OREML output containing percent variance explained in external data and standard error
Katelyn Queen, kjqueen@usc.edu
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Queen K, Nguyen MN, Gilliland F, Chun S, Raby BA, Millstein J. ACDC: a general approach for detecting phenotype or exposure associated co-expression. Frontiers in Medicine (2023) 10. doi:10.3389/fmed.2023.1118824.
OSCA software - https://yanglab.westlake.edu.cn/software/osca/
#load CCA package for example dataset
library(CCA)
# load dataset
data("nutrimouse")
# run function; input absolute path to OSCA software before running
## Not run: OSCA_singleValue(df = nutrimouse$gene,
externalVar = as.numeric(nutrimouse$diet),
oscaPath = "pathHere")
## End(Not run)