summary.jtGWAS {jtGWAS} | R Documentation |
Summary method for jtGWAS results.
## S3 method for class 'jtGWAS' summary(object, marker2Print=1:10, SNP2Print=1:10, printP=TRUE, outTopN=NA, subObj=FALSE, ...)
object |
A jtGWAS object that is the return of method |
marker2Print |
Either a numeric or character vector that indicates the desired dependent variables to print. The default is 1:10. Set to |
SNP2Print |
Either a numeric or character vector that indicates the desired independent variables to print. If |
printP |
A boolean indicating whether to print the p-value ( |
outTopN |
An integer specifying the number of top hits to print in the summary, if the statistics were not sorted during the statistics evaluation (i.e., if |
subObj |
A boolean indicating whether to return a |
... |
Additional arguments affecting the summary produced. |
If subObj=TRUE
, this method returns a jtGWAS
object matching the subset of statistics from object
that are being printed. For example, if object
is not sorted by top hits, summary(object, outTopN=10, subObj=TRUE)
will print the summary and return a subset of object
that contains only the top 10 SNPs for each marker. If subObj=FALSE
, nothing is returned.
This function prints a matrix or paired columns of SNP IDs and statistics/p-values to the log.
# Generate dummy data num_patient <- 100 num_marker <- 10 num_SNP <- 500 set.seed(12345); X_pat_mak <- matrix(rnorm(num_patient*num_marker), num_patient, num_marker) G_pat_SNP <- matrix(rbinom(num_patient*num_SNP, 2, 0.5), num_patient, num_SNP) colnames(X_pat_mak) <- colnames(X_pat_mak, do.NULL=FALSE, prefix="Mrk:") colnames(G_pat_SNP) <- colnames(G_pat_SNP, do.NULL=FALSE, prefix="SNP:") res <- jtGWAS(X_pat_mak, G_pat_SNP, outTopN=5) summary(res, marker2Print=c("Mrk:1","Mrk:2"), SNP2Print=1:5, printP=FALSE) summary(res, marker2Print=NA, SNP2Print=1:5, printP=FALSE) res <- jtGWAS(X_pat_mak, G_pat_SNP, outTopN=NA) summary(res, marker2Print=1:10, SNP2Print=1:10, printP=TRUE) summary(res, marker2Print=c("Mrk:1","Mrk:2"), SNP2Print=c("SNP:1","SNP:2"), printP=TRUE) res <- jtGWAS(X_pat_mak, G_pat_SNP, outTopN=NA, standardized=FALSE) summary(res, outTopN=10)