traseR {traseR} | R Documentation |
Perform GWAS trait-associated SNP enrichment analyses in genomic intervals using different approaches
traseR(snpdb, region, snpdb.bg=NULL, keyword = NULL, rankby = c("pvalue", "odds.ratio"), test.method = c("binomial", "fisher","chisq", "nonparametric"), alternative = c("greater", "less", "two.sided"), ntimes=100,nbatch=1, trait.threshold = 0, traitclass.threshold=0, pvalue = 1e-3)
snpdb |
A GRange object.
It could be GWAS trait-associated SNPs downloaded from up-to-date dbGaP and NHGRI public database. It is maintained to be updated to the latest version. The data frame contains the following columns, |
region |
A GRange object or data frame, which is genomic intervals with three columns, chromosome, genomic start position, genomic end position. |
snpdb.bg |
A GRange object contains non-trait-associated SNPs. They are treated as background for statistical testing instead of whole genome as background if specified. |
keyword |
The keyword is used when specific trait is of interest. If |
rankby |
Traits could be ranked by either p-value or adds.ratio based on the enrichment level of trait-associated SNPs in genomic intervals. |
test.method |
Several hypothesis testing options are provided: |
alternative |
Indicate the alternative hypothesis. If |
ntimes |
The number of shuffling time for one batch. See |
nbatch |
The number of batches. The product of |
trait.threshold |
Test traits with number of SNPs more than the threshold. |
traitclass.threshold |
Test trait class with number of SNPs more than the threshold. |
pvalue |
SNPs with p-value less than this threshold are used for analyses. |
Return a list that contains three data frames. One data frame tb.all
contains the results of
enrichment analyses for all trait-associated SNPs in genomic intervals.
Another data frame tb1
contains the results of enrichment analyses for each trait-associated SNPs
in genomic intervals separately.
Another data frame tb2
contains the results of enrichment analyses for each trait-class-associated SNPs
in genomic intervals separately.
The data frame tb1
has columns,
Trait |
Name of trait |
p.value |
P-value calculated from hypothesis testing |
q.value |
Adjusted p-value from multiple testing using FDR correction |
odds.ratio |
Odds ratio calculated based on number of trait-associated SNPs in genomic intervals, number of trait-associated SNPs across whole genome, genomic intervals size (bps) and genome size (bps) |
taSNP.hits |
Number of trait-associated SNPs in genomic intervals |
taSNP.num |
Number of SNPs for specific trait |
Li Chen <li.chen@emory.edu>, Zhaohui S.Qin<zhaohui.qin@emory.edu>
print.traseR
data(taSNP) data(Tcell) x=traseR(snpdb=taSNP,region=Tcell) print(x)