ucscannot: Functional Annotation of _SNP_s Chosen
In Yuande/GMRP: GWAS-based Mendelian Randomization and Path Analyses

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function is used to give proportion of SNPs derived from functional elements of genes.

1	ucscannot(UCSCannot,SNPn,A=3,B=1.9,C=1.3,method=1)

`UCSCannot`	annotation data obtained by performing `SNP` tools.
`SNPn`	numeric parameter for number of `SNP`s contained in `UCSCannot`
`A`	numeric parameter for title size, default=2.5
`B`	numeric parameter for label size, default=1.5
`C`	numeric parameter for `labelrad` distance,default=0.1
`method`	numeric parameter for choosing figure output methods. It has two options: method=1 has no legend but color and pie components are labeled with gene elements, method=2 has legend over pie. The default = 1.

SNPs chosen by performing mktable should be copied to Batch Query Box in SNP annotation tool. After setting parameters and running by clicking run button, SNP annotation data will be obtained after running for a while. Consequence sheet of UCSC should be copied to excel sheet,"Predicted function" column name is changed to "function_unit" name and save it as csv format. These parametric defaults are used as graph image for publication, user can expand image to the maximum size and copy it to powerpoint that will give ideal effect. User also can use R packagelink{VariantAnnotation} to get SNP annotation result but the result must be constructed a table with function_unit column listing gene elements and Symbol column listing genes, otherwise, ucscannot will get an error.

Create a color pie3D diagram and return a set of numeric values: proportions of code region, intron,3'and 5' UTRs and upstream and downstream etc.

This function just need data of "Predicted function" and "symbol", so the other column data in UCSCannot do not impact the results of analysis.

Yuan-De Tan tanyuande@gmail.com

http://snp-nexus.org/index.html

mktable, pie3D,link{VariantAnnotion}

data(SNP368annot.data)
SNP368<-as.data.frame(SNP368annot.data)
ucscannot(UCSCannot=SNP368,SNPn=368,A=1.5,B=1,C=1.3)
ucscannot(UCSCannot=SNP368,SNPn=368,A=1.5,B=1,C=1.3,method=2)