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 XP-CLR version 1.0 10-30-2009 (linux)

Hua Chen
hchen@genetics.med.harvard.edu


The XP-CLR package implements a composite likelihood method for detecting 
selective sweeps via the differentiation of two populations. 


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Executables and scource code:
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All C executables are in the bin/ directory.

We have placed source code for all C executables in the src/ directory, 
for users who wish to modify and recompile our programs.  For example, 
to recompile the eigenstrat program, type
"cd src"
"make"      
"make install"


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Command line:
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XPCLR -xpclr genofile1 genofile2 mapfile outputFile -w1 snpWin gridSize chrN 
       -p corrLevel
-xpclr:		specify the input file format.[XpCLR accepts several other 
                 input formats, but currently they haven't been checked 
                 carefully yet.]
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.
-w1:		set it to "-w1"
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
                 regions, 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.
-p: "-p1": 	specify this if the genotype data is already phased.
    "-p0": 	specify this if the genotype data is unphased.
		The phase information of the genotype is used only if 
                 corrLevel is set to be >0. When corrLevel >0, the XP-CLR score 
                 is estimated using a weighted scheme. The weights come from
                 the pairwise correlation between SNPs in the reference pop.
                 If "p1", the phased data will be used to estimate pairwise 
                 correlation coefficient directly; if "p0", pairwise correlation
                 coefficients are estimated with an EM algorithm.  
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 -xpclr CEU.9 YRI.9 snp.9 xpclr.9 -w1 0.005 200 2000 1 -p0 0.95

which means, a scan for selection on the genotype data from CEU.9 with YRI.9 as 
a reference, the output file is named with appendix "xpclr.9". A set of grid 
points as the putative selected allele positions are placed along the chromosome
with a spacing of 2kb, the sliding window size is 0.5cM around the gird points. 
If the number of SNPs within a window is beyond 200, some SNPs will be randomly
dropped to control for the SNP number. A weighted CLR scheme is adopted in
estimating XPCLR--the pairwise correlation coefficients (r2) of SNPs from the 
reference population are used to give weights. When r2 >0.95, CLR scores for 
these two SNPs are down-weighted. The genotype data of input is unphased, thus 
r2 coefficients are estimated via a EM algorithm. 
  
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Input/output format:
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.geno file:
each row contains the genotype of a single SNP
for example:

1 0 1 1 9 9
1 1 1 0 0 0

which contains two SNPs from 3 individuals. The first two columns are the two 
alleles of individual #1. 1 and 0 correspond to two allele types. 9 denotes 
missing data. The data could be phased or unphased. If it is phased, then each
column stands for alleles from the same haplotype. Otherwise, the two alleles
of an individual are placed arbitrarily.

NOTE: The format is different from eigenstrat .geno file!
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.snp file:
each row contains information on a SNP:
SNPName chr# GeneticDistance(Morgan) PhysicalDistance(bp) RefAllele TheOtherAllele
for example:
rs465423 1 0.042681 4268076 T C

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output file:
chr# grid# #ofSNPs_in_window physical_pos genetic_pos XPCLR_score max_s


The output file can be used to make plots with other softwares, eg, R, Matlab.

To make a plot of XP-CLR along the chromosome using matlab:
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xpclrScore=load('fileNameofOutput');
plot(xpclrScore(:,4),xpclrScore(:,6),'.');

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