Package 'traseR'

Title: GWAS trait-associated SNP enrichment analyses in genomic intervals
Description: traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
Authors: Li Chen, Zhaohui S.Qin
Maintainer: li chen<[email protected]>
License: GPL
Version: 1.37.0
Built: 2024-10-31 06:26:54 UTC
Source: https://github.com/bioc/traseR

Help Index

GWAS trait-associated SNP enrichment analyses in genomic intervals

Description

Perform GWAS trait-associated SNP enrichment analyses in genomic intervals. Explore and visualize the results.

Details

Package: traseR
Type: Package
Version: 1.0
Date: 2015-11-18
License: GPL

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

Sampled SNPs from all SNPs of CEU population in 1000 genome project

Description

A GRange object CEU contains 5% of all SNPs from CEU by controling genome-wide density is the same as all SNPs from CEU

Usage

data(CEU)

Value

The data frame CEU contains three columns,

SNP_ID

SNP rs number
seqnames

Chromosome number associated with rs number
ranges

Chromosomal position, in base pairs, associated with rs number

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

Visualize of trait-associated SNPs

Description

These are a group of functions to generate plot to visualize the trait-associated SNPs.

Usage

plotContext(snpdb, region=NULL, keyword = NULL, pvalue = 1e-3)

plotPvalue(snpdb, region=NULL, keyword = NULL, plot.type = c("densityplot", "boxplot"), pvalue = 1e-3, xymax = 50)

plotSNP(snpdb, snpid, ext = 10000)

plotGene(snpdb, gene, ext = 10000)

plotInterval(snpdb,interval,ext = 10000)

Arguments

snpdb

A GRange object or data frame, which is 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,Trait,SNP,p.value,Chr,Position,Context,GENE_NAME,GENE_START,GENE_END,GENE_STRAND. The data frame is in data subdirectory. Users are free to add more SNP records to the data frame for practical use.

region

A data frame, which is genomic intervals with three columns, chromosome, genomic start position, genomic end position.

keyword

The keyword is used when specific trait is of interest. If keyword is specified, only the SNPs associated to the trait are used for analyses. Otherwise, all traits will be analyzed.

snpid

SNP rs number
gene

Gene name
pvalue

SNPs with p-value less than this threshold are used for analyses.

plot.type

Either "densityplot" or "boxplot"
ext

Bp extended upstream and downstream
xymax

The maximum range on x-axis and y-axis
interval

A data frame, genomic interval:chromosome, genomic start position, genomic end position

Value

plotContext

A pie plot with the distribution of SNP function class
plotPvalue

A density plot of -logPvalue of trait-associated SNPs
plotSNP

A plot of trait-associated SNP on chromosome
plotGene

A plot with the gene and possible nearby trait-associated SNPs

plotInterval

A plot with chromosome interval with possible nearby genes and trait-associated SNPs

Author(s)

Li Chen <[email protected]>, Zhaohui Qin<[email protected]>

Examples

data(taSNP)
	plotContext(snpdb= taSNP,keyword="Autoimmune")
	plotGene(snpdb= taSNP,gene="ZFP92",ext=50000)
	plotSNP(snpdb= taSNP,snpid="rs766420",ext=50000)
	plotInterval(snpdb= taSNP,data.frame(chr="chrX",start=152633780,end=152737085))

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

x

Object returned from traseR
isTopK1

If isTopK1 is TRUE, topK1 traits are printed; otherwise, traits with p-value below Bonferroni correction threshold are printed. Default is FALSE.
topK1

Top K1 traits are printed. Default is 10.
isTopK2

If isTopK2 is TRUE, topK2 trait class are printed; otherwise, trait class with p-value below Bonferroni correction threshold are printed. Default is FALSE.
topK2

Top K2 trait class are printed. Default is 10.
trait.threshold

Traits above this threshold are reported. Default is 10.
traitclass.threshold

Trait class above this threshold are reported. Default is 10.
...

Other parameters to print

Value

Print a data frame of traits ranked by p-value

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

Examples

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

Retrieve trait-associated SNPs based

Description

These are a group of functions to retrieve the trait-associated SNPs based on input

Usage

queryKeyword(snpdb, region=NULL, keyword = NULL, returnby = c("SNP_ID", "trait"), pvalue = 1e-3)

queryGene(snpdb, genes = NULL)

querySNP(snpdb, snpid, region = NULL)

Arguments

snpdb

A GRange object or data frame, which is 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,Trait,SNP_ID,p.value,Chr,Position,Context,GENE_NAME,GENE_START,GENE_END,GENE_STRAND. The data frame is in data subdirectory. Users are free to add more SNP records to the data frame for practical use.

region

A data frame, which is genomic intervals with three columns, chromosome, genomic start position, genomic end position.

keyword

The keyword is used when specific trait is of interest. If keyword is specified, only the SNPs associated to the trait are used for analyses. Otherwise, all traits will be analyzed.

snpid

SNP rs number
genes

Gene name
pvalue

SNPs with p-value less than this threshold are used for analyses.

returnby

Either SNP or trait. If returnby is specified as 'SNP_ID', a data frame based on 'SNP_ID' is returned. If returnby is specified as 'trait', a data frame based on 'trait' is returned.

Value

queryKeyword: Return a data frame of traits containing the keyword queryGene: Return a data frame of traits associated with the gene querySNP: Return a data frame of traits associated with the SNP

Author(s)

Li Chen <[email protected]>, Zhaohui Qin<[email protected]>

Examples

data(taSNP)
	data(Tcell)
	x=queryKeyword(snpdb=taSNP,region=Tcell,keyword="Autoimmune",returnby="SNP_ID")
	x=queryGene(snpdb=taSNP,genes=c("AGRN","UBE2J2","SSU72"))
	x=querySNP(snpdb=taSNP,snpid=c("rs3766178","rs880051"))

trait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser

Description

A GRange object taSNP contains trait-associated SNPs from dbGaP and NHGRI downloaded from Association Results Browser.

Usage

data(taSNP)

Value

The data frame taSNP contains the following columns

Trait

Trait
Trait Class

Trait class which is formed based on the phenotype tree. Close traits are grouped together to form one class
SNP_ID

SNP rs number
p.value

GWAS SNP p-value
seqnames

Chromosome
ranges

Chromosome position
Context

SNP functional class
GENE_NAME

Nearest gene name
GENE_START

Gene start genomic position
GENE_END

Gene end genomic position
GENE_STRAND

Gene strand

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

linkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI

Description

A GRange object taSNPLD contains linkage disequilibrium (>0.8) SNPs of all trait-associated SNPs from dbGaP and NHGRI.

Usage

data(taSNPLD)

Value

The data frame taSNPLD contains four columns,

SNP_ID

SNP rs number
seqnames

Chromosome number associated with rs number
ranges

Chromosomal position, in base pairs, associated with rs number
Trait

Trait the SNP is associated with
Trait Class

Trait class which is formed based on the phenotype tree. Close traits are grouped together to form one class

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

Peak regions of H3K4me1 in Peripheral blood T cell

Description

A GRange object Tcell contains three columns: chromosome, genomic start position and genomic end position.

Usage

data(Tcell)

Value

The data frame Tcell contains three columns,

seqnames

Chromosome id
ranges

Chromosome position

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

TRait-Associated SNP EnRichment analyses

Description

Perform GWAS trait-associated SNP enrichment analyses in genomic intervals using different approaches

Usage

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)

Arguments

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,Source,Trait,SNP,p.value,Chr,Position,Context,GENE_NAME,GENE_START,GENE_END,GENE_STRAND. The data frame is in data subdirectory. Users are free to add more SNP records to the data frame for practical use. It could also be a data frame with columns as, SNP,Chr,Position.

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 keyword is specified, only the SNPs associated to the trait are used for analyses. Otherwise, all traits will be analyzed.

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: binomial(binomial test),fisher(Fisher's exact test),chisq(Chi-squared test),chisq(nonparametric test). Default is binomial(binomial test)

alternative

Indicate the alternative hypothesis. If greater, test if the genomic intervals are enriched in trait-associated SNPs than background. If less, test if the genomic intervals are depleted in trait-associated SNPs than background. If two.sided, test if there is difference between the enrichment of trait-associated SNPs in genomic intervals and in background.

ntimes

The number of shuffling time for one batch. See nbatch.

nbatch

The number of batches. The product of ntimes and nbatch is the total number of shuffling time.

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.

Details

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.

Value

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

Author(s)

Li Chen <[email protected]>, Zhaohui S.Qin<[email protected]>

See Also

print.traseR

Examples

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