Print the outcome of taSNP enrichment analyses

Description

Print the outcome of taSNP enrichment analyses. Print the overall taSNP enrichment, trait-specific taSNP enrichment,trait-class-specific taSNP enrichment.

Usage

	## S3 method for class 'traseR'
print(x,isTopK1=FALSE,topK1=10,isTopK2=FALSE,topK2=10,trait.threshold=10,traitclass.threshold=10,...)

Arguments

Value

Print a data frame of traits ranked by p-value

Author(s)

Li Chen <li.chen@emory.edu>, Zhaohui S.Qin<zhaohui.qin@emory.edu>

Examples

	data(taSNP)
	data(Tcell)
	x=traseR(snpdb=taSNP,region=Tcell)
	print(x)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(traseR)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/traseR/print.traseR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: print.traseR
> ### Title: Print the outcome of taSNP enrichment analyses
> ### Aliases: print.traseR
> 
> ### ** Examples
> 
> 	data(taSNP)
> 	data(Tcell)
> 	x=traseR(snpdb=taSNP,region=Tcell)
There are  128094211 bp in the query region, accounting for  0.0421875469310327  of the genome.
There are  573 traits in the analysis.
There are  33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!
> 	print(x)
There are 573 traits in the test.
The overall functional SNP enrichment test results are:
  Trait       p.value odds.ratio taSNP.hits taSNP.num
1   All 3.788373e-233   2.134717       2625     30553
The trait-associated SNP enrichment test results are:
                            Trait      p.value      q.value odds.ratio
67                Behcet Syndrome 4.400406e-23 2.521433e-20   6.306579
172     Diabetes Mellitus, Type 1 1.704981e-11 4.884769e-09   5.045263
340 Lupus Erythematosus, Systemic 6.159346e-09 1.176435e-06   3.902195
49          Arthritis, Rheumatoid 1.442123e-07 2.065841e-05   5.126637
379            Multiple Sclerosis 1.644125e-05 1.884167e-03   2.905210
62            Autoimmune Diseases 5.201529e-05 4.967461e-03  15.892575
    taSNP.hits taSNP.num
67          59       274
172         33       185
340         32       223
49          20       112
379         26       236
62           6        15
The trait-class-associated SNP enrichment test results are:
                           Trait_Class      p.value      q.value odds.ratio
17              Immune System Diseases 3.729169e-35 1.143835e-33   3.658860
31 Skin and Connective Tissue Diseases 6.932335e-35 1.143835e-33   3.916319
32             Stomatognathic Diseases 1.041455e-22 1.145601e-21   5.675922
14                        Eye Diseases 3.479491e-18 2.870580e-17   3.313308
11           Digestive System Diseases 4.362324e-14 2.879134e-13   3.040672
7              Cardiovascular Diseases 3.008551e-11 1.654703e-10   1.602762
13           Endocrine System Diseases 6.933337e-09 3.268573e-08   2.068149
24  Nutritional and Metabolic Diseases 4.763509e-08 1.964948e-07   2.068673
21            Musculoskeletal Diseases 3.118359e-05 1.143398e-04   2.716680
23             Nervous System Diseases 5.549981e-05 1.831494e-04   1.495744
16        Hemic and Lymphatic Diseases 1.649261e-04 4.947782e-04   3.596622
22                           Neoplasms 3.372076e-04 9.273210e-04   1.580636
30          Respiratory Tract Diseases 6.507770e-04 1.651972e-03   2.121839
   taSNP.hits taSNP.num
17        155      1122
31        142       970
32         63       318
14         87       689
11         74       633
7         253      3850
13         89      1076
24         79       956
21         27       260
23        122      1988
16         15       115
22         76      1181
30         29       349
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>