| concur {CONCUR} | R Documentation |
Copy Number Profile Curve-Based Association Test
Description
Implements a kernel-based association test for CNV aggregate analysis in a certain genomic region (e.g., gene set, chromosome, or genome) that is robust to the within-locus and across-locus etiologoical heterogeneity, and bypass the need to define a "locus" unit for CNVs.
Usage
concur(
cnv,
X,
pheno,
phenoY,
phenoType,
...,
nCore = 1L,
outFileKernel = NULL,
verbose = TRUE
)
Arguments
cnv |
A character or data.frame object. If character, the name of the data file containing the CNV data (with a header). If data.frame, the CNV data. The data must contain the following columns: "ID", "CHR", "BP1", "BP2", "TYPE", where "ID" is a unique patient id, "CHR" is the CNV chromosome, "BP1" is the start location in base pairs or kilo-base pairs, "BP2" is the end location in base pairs or kilo-base pairs, and "TYPE" is the CNV copy number. |
X |
A character or data.frame object. If character, the name of the data file containing the covariate data (with a header). If data.frame, the covariate data. The data must contain a column titled "ID" containing a unique patient id. This column must contain the patient identifiers of the CNV data specified in input cnv; however, it can contain patient identifiers not contained in cnv. Further, inputs X and pheno must contain the same patient identifiers. Categorical variables must be translated into design matrix format. |
pheno |
A character or data.frame object. If character, the name of the data file containing the phenotype data (with a header). If data.frame, the phenotype data. The data must contain a column titled "ID" containing a unique patient id. This column must contain the patient identifiers of the CNV data specified in input cnv; however, it can contain patient identifiers not contained in cnv. Further, inputs X and pheno must contain the same patient identifiers. |
phenoY |
A character object. The column name in input pheno containing the phenotype of interest. |
phenoType |
A character object. Must be one of of {"bin", "cont"} indicating if input phenoY (i.e., the phenotype of interest) is binary or continuous. |
... |
Ignored. Included to require named inputs. |
nCore |
An integer object. If nCore > 1, package parallel is used to calculate the kernel. Though the methods of package CompQuadForm dominate the time profile, setting nCore > 1L can improve computation times. |
outFileKernel |
A character object or NULL. If a character, the file in which the kernel is to be saved. If NULL, the kernel is returned by the function. |
verbose |
A logical object. If TRUE, progress information is printed to the screen. |
Details
The CNV data must adhere to the following conditions:
CNVs must be at least 1 unit long.
CNVs cannot end at the exact location another begins
Violations of these conditions typically occur when data are rounded to a desired resolution. For example
ID CHR BP1 BP2 TYPE 1 13 10112087 10112414 3
becomes upon rounding to kilo
ID CHR BP1 BP2 TYPE 1 13 10112 10112 3 .
These cases should either be discarded or modified to be of length 1, e.g.,
ID CHR BP1 BP2 TYPE 1 13 10112 10113 3 .
As an example of condition 2
ID CHR BP1 BP2 TYPE 1 13 100768 101100 3 1 13 101100 101299 1
should be modified to one of
ID CHR BP1 BP2 TYPE 1 13 100768 101100 3 1 13 101101 101299 1
or
ID CHR BP1 BP2 TYPE 1 13 100768 101099 3 1 13 101100 101299 1 .
Additionally,
ID CHR BP1 BP2 TYPE 1 13 100768 101100 3 1 13 101100 101299 3
should be combined as
ID CHR BP1 BP2 TYPE 1 13 100768 101299 3 .
Value
A list containing the kernel (or its file name) and the p-value.
References
Brucker, A., Lu, W., Marceau West, R., Yu, Q-Y., Hsiao, C. K., Hsiao, T-H., Lin, C-H., Magnusson, P. K. E., Holloway, S. T., Sullivan, P. F., Szatkiewicz, J. P., Lu, T-P., and Tzeng, J-Y. Association testing using Copy Number Profile Curves (CONCUR) enhances power in copy number variant analysis. <doi:10.1101/666875>.
Examples
data(cnvData)
# limit data for examples
exCNV <- cnvData$ID %in% paste0("P", 1:150)
exCOV <- covData$ID %in% paste0("P", 1:150)
exPHE <- phenoData$ID %in% paste0("P", 1:150)
# binary phenoType
results <- concur(cnv = cnvData[exCNV,],
X = covData[exCOV,],
pheno = phenoData[exPHE,],
phenoY = 'PHEB',
phenoType = 'bin',
nCore = 1L,
outFileKernel = NULL,
verbose = TRUE)
# continuous phenoType
results <- concur(cnv = cnvData[exCNV,],
X = covData[exCOV,],
pheno = phenoData[exPHE,],
phenoY = 'PHEC',
phenoType = 'cont',
nCore = 1L,
outFileKernel = NULL,
verbose = TRUE)