Trans Meta Manual

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Package ‘TransMeta’
October 4, 2015
Type Package
Title A novel random effect model for GWAS trans-ethnic meta-analysis
Version 0.2
Date 2015-04-29
Author Jingchunzi Shi, Seunggeun Lee
Maintainer Jingchunzi (Jing) Shi 
Description A kernel regression based random effect model for testing single variant association in GWAS trans-ethnic meta-analysis.
License GPL (>= 2)
Depends SKAT, R (>= 2.13.0)

R topics documented:
TransMeta-package
F_ST . . . . . . .
get_K_Fst . . . . .
get_K_indep . . . .
Get_TransMeta . .
G_ind . . . . . . .

TransMeta-package

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A novel random effect model for GWAS trans-ethnic meta-analysis

Description
This package implements the kernel machine based random effect model for testing single variant
association in trans-ethnic meta-analysis
Details
Package:
Type:
Version:
Date:
License:

TransMeta
Package
0.2
2015-4-29
GPL (>= 2)

1

2

F_ST
This package implements the kernel machine based random effect model for single variant test in
GWAS trans-ethnic Meta-analysis. In order to get p-value of the association test, the user should
provide the effect-size estimates, standard error estimates and kernel matrix K in the Get_TransMeta
function.

Author(s)
Jingchunzi Shi, Seunggeun Lee
Maintainer: Jingchunzi (Jing) Shi 

F_ST

K matrix of the genetic similarity kernel structure for 9 ancestry
groups from HMP3 data.

Description
The kernel matrix K of the genetic similarity kernel structure for the 9 ancestry groups from HMP3
data. The 9 ancestry groups are (in the following order): CEU - Utah residents with Northern and
Western European ancestry from the CEPH collection; CHD - Chinese in Metropolitan Denver,
Colorado; GIH - Gujarati Indians in Houston, Texas; JPT_CHB - Japanese in Tokyo, Japan & Han
Chinese in Beijing, China; LWK - Luhya in Webuye, Kenya; MXL - Mexican ancestry in Los
Angeles, California; MKK - Maasai in Kinyawa, Kenya; TSI - Toscani in Italia; YRI - Yoruba in
Ibadan, Nigeria.
Usage
data(F_ST)
Details
A 9 × 9 kernel matrix of the genetic similarity kernel structure for the 9 ancestry groups from
HMP3 data. The (i,j)-th entry value in the matrix is obtained as a function of the pair-wise F.st
value between the i-th ancestry group and the j-th ancestry group. Order of the 9 ancestry groups is
arranged as follows: CEU, CHD, GIH, JPT+CHB, LWK, MEX, MKK, TSI, YRI.
Source
The pair-wise F.st values are obtained from Table S6 in:
http://hapmap.ncbi.nlm.nih.gov/downloads/presentations/nature09298-s1.pdf
Examples
data(F_ST)

get_K_Fst

get_K_Fst

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Construct the genetic similarity kernel matrix K

Description
Construct the genetic similarity kernel matrix K for testing the single variant association in transethnic meta-analysis.
Usage
get_K_Fst(FileName)
Arguments
FileName

A vector of characters that list the file names of summary statistics for each
GWAS and the file name of a data file that identifies each study’s corresponding
ancestry group.

Details
Please refer to the Vignettes PDF manual for details of the FileName argument.
Value
Returns the genetic similarity kernel matrix K for testing the single variant association in transethnic meta-analysis. For example, the returned matrix can be used for the argument K in the
Get_TransMeta function.

get_K_indep

Construct the group-wise independent kernel matrix K

Description
Construct the group-wise independent kernel matrix K for testing the single variant association in
trans-ethnic meta-analysis.
Usage
get_K_indep(FileName)
Arguments
FileName

A vector of characters that list the file names of summary statistics for each
GWAS and the file name of a data file that identifies each study’s corresponding
ancestry group.

Details
Please refer to the Vignettes PDF manual for details of the FileName argument.

4

Get_TransMeta

Value
Returns the group-wise independent kernel matrix K for testing the single variant association in
trans-ethnic meta-analysis. For example, the returned matrix can be used for the argument K in the
Get_TransMeta function.
Examples
## Please refer to the example in the Vignettes PDF manual

Get_TransMeta

Single variant association test in the GWAS trans-ethnic meta-analysis

Description
Implementation of the kernel regression based random effect model for the single variant association
test in the GWAS trans-ethnic meta-analysis
Usage
Get_TransMeta(FileName, type = "effect size", K.type = "Fst", K = NULL,
r.all = c(0, 0.09, 0.25, 1), method = "liu")
Arguments
FileName

A vector of characters that list the file names of summary statistics for each
GWAS and the file name of a data file that identifies each study’s corresponding
ancestry group. Please refer to the Vignettes PDF manual for its details.

type

The default value is "effect size", which specifies that the input summary statistics are effect size based; otherwise, the Z-score based summary statistics will
be used.

K.type

The default value is "Fst", which specifies that the K matrix is of the genetic similarity kernel structure; otherwise, the K matrix would take the group-independent
kernel structure.

K

A square matrix for the kernel matrix K, for example, K can be constructed
based on the HapMap3 data using the get_K_Fst function. If the user does not
provide a matrix for this argument, then the K matrix will be constructed based
on the input data (to estimate F.st) with its specified structure from the K.type
argument.

r.all

A vector of possible values of ρ to be used, default = c(0, 0.09, 0.25, 1).

method

A method to compute the p-value (default= ‘liu’). ‘davies’ represents an exact
method that computes the p-value by inverting the characteristic function of the
mixture chisq; ‘liu’ represents an approximation method that matches the first
3 moments; ‘liu.mod ’ represents modified ‘liu’ method that matches kurtosis
instead of skewness to improve tail probability approximation.

G_ind

5

Value
SNP

The SNP id for each variant

Pval

p-value from TransMeta for the association test

Pval_rho

p-value of the score test for each ρ in the ‘r.all ’ argument

Opt_rho

the optimal ρ in the ‘r.all’ argument which results in smallest p-value for the
score test

Examples
## Please refer to the example in the Vignettes PDF manual

G_ind

K matrix of the group-wise independent kernel structure for the 9 ancestry groups from HMP3 data.

Description
K matrix of the group-wise independent kernel structure for the 9 ancestry groups from HMP3 data.
The 9 ancestry groups are (in the following order): CEU - Utah residents with Northern and Western
European ancestry from the CEPH collection; CHD - Chinese in Metropolitan Denver, Colorado;
GIH - Gujarati Indians in Houston, Texas; JPT_CHB - Japanese in Tokyo, Japan & Han Chinese
in Beijing, China; LWK - Luhya in Webuye, Kenya; MXL - Mexican ancestry in Los Angeles,
California; MKK - Maasai in Kinyawa, Kenya; TSI - Toscani in Italia; YRI - Yoruba in Ibadan,
Nigeria.
Usage
data(G_ind)
Details
A 9 × 9 diagonal matrix. The entries correspond to the order of the 9 ancestry groups as listed
above.
Examples
data(G_ind)



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