How to cite
Chen H, Patterson N, Reich D. Population differentiation as a test for selective
sweeps[J]. Genome Research, 2010, 20(3):393. [PMID=20086244]
Help information
XPCLR Version 1
Usage:
XPCLR -genofile1 -genofile2 -mapfile -outputfile -gWin -snpWin -gridSize -chrN -p
OPTIONS:
XPCLR -genofile1 -genofile2 -mapfile -outputfile -gWin -snpWin -gridSize -chrN -p
OPTIONS:
genofile1: genotype input for object population
genofile2: genotype input for reference population
mapfile: snp information file (for SNPs from a single chromosome)
outputfile: The format is illustrated in next section.
gWin: the size of a window (in units of Morgan). If the window size is not too small, the performance of XPCLR doesn't depend on the size. A reasonable choice is 0.005.
snpWin: maximum # of SNPs within a window. XPCLR score depends on the number of SNPs. To make the XP-CLR scores comparable between
egions, it is necessary to control the maximum number of SNPs within a single window. The choice of snp # depends on the SNP density of your data.
gridSize: the spacing between two grid points. It is in unit of bp.
chrN: the chromosome number.
corrLevel: the range of its value is on [0 1]. If it is on (0 1], this corrLevel value is used as a criterion in the weighted composite likelihood ratio test. If two SNPs are highly correlated (r2 > corrLevel), their contribution to XPCLR is down-weighted. If corrLevel is set to be 0, XPCLR is estimated un-weightedly.
One example of command line:
XPCLR -genofile1 CEU.9 -genofile2 YRI.9 -mapfile snp.9 -outputfile xpclr.9 -gWin 0.005 -snpWin 200 -gridSize 2000 -chrN 1 -p 0.95
genofile2: genotype input for reference population
mapfile: snp information file (for SNPs from a single chromosome)
outputfile: The format is illustrated in next section.
gWin: the size of a window (in units of Morgan). If the window size is not too small, the performance of XPCLR doesn't depend on the size. A reasonable choice is 0.005.
snpWin: maximum # of SNPs within a window. XPCLR score depends on the number of SNPs. To make the XP-CLR scores comparable between
egions, it is necessary to control the maximum number of SNPs within a single window. The choice of snp # depends on the SNP density of your data.
gridSize: the spacing between two grid points. It is in unit of bp.
chrN: the chromosome number.
corrLevel: the range of its value is on [0 1]. If it is on (0 1], this corrLevel value is used as a criterion in the weighted composite likelihood ratio test. If two SNPs are highly correlated (r2 > corrLevel), their contribution to XPCLR is down-weighted. If corrLevel is set to be 0, XPCLR is estimated un-weightedly.
One example of command line:
XPCLR -genofile1 CEU.9 -genofile2 YRI.9 -mapfile snp.9 -outputfile xpclr.9 -gWin 0.005 -snpWin 200 -gridSize 2000 -chrN 1 -p 0.95
Parameters Description
| -IN1: | Genotype file |
| genotype input for object population |
| -IN2: | Genotype file |
| genotype input for reference population |
| -M: | Map file |
| snp information file (for SNPs from a single chromosome) |
| -W: | The size of a window |
| the size of a window (in units of Morgan). If the window size is not too small, the performance of XPCLR doesn't depend on the size. A reasonable choice is 0.005. |
| -SNP: | Maximum # of SNPs within a window |
| the choice of snp # depends on the SNP density of your data. |
| -G: | The spacing between two grid points |
| it is in unit of bp. |
| -C: | The chromosome number. |
| the chromosome number. |
| -P: | CorrLevel |
| the range of its value is on [0 1]. |
Evolution Data Analysis
- GeneTree 1.3
- TreeSAAP 3.2
Data visualization
- Bar Chart
- Line Chart
- Histogram Chart
About us
- About us
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Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB13000000
Maintained by BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences.