Ñò ‘Mc@s|ddklZlZlZyddkZeZWn eZnXd„Zd„Z d„Z d„Z d„Z d„Z dS( iÿÿÿÿ(tlogtsqrttexpNcCs*t|ƒtt|ƒt|ƒƒ}|S(sC returns log likelihood for one pair of observed vs. expected. (tfloatR(tobservedtexpectedtscore((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pytllScore)s&cCs6t|ƒt|ƒtt|ƒ|d|ƒ}|S(s¢ returns (observed - expected)/(standard deviation), where the standard deviation is calculated assuming normality as sqrt(obs * prob * (1 - prob)). i(RR(RRtprobR((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pytzScore0s2cCs||S(N((tlengthR((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pyR8scCsgt|ƒ}d|dd|}dtdtd||ƒƒd}|djod|}n|S(s¨ approximation for converting from zvalue to P-value using Hamaker's formula as described in Zar (App18). This is dependable down to abs(z) ~ 0.2 g˜nƒÀÊé?ig;ßO—n’?iÿÿÿÿii(tabsRR(tzvaluetztctpval((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pytpvalue<s  & cCs)toti||ƒSt||ƒSdS(N(thasStatExtensiont_stattpearsonCorrelationtlocalPearsonCorrelation(tcolAtcolB((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pyRKsc Cs6d}d}t|ƒ}|t|ƒjot|ƒ}nx0t|ƒD]"}|||7}|||7}qHW||:}||:}d}d}d}xnt|ƒD]`}|||||||7}|||||||7}|||||||7}q¡W|djp |djodS|t||ƒS(Ng(tlentrangeR( RRtmeanAtmeanBR tindext numeratort denominatorAt denominatorB((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pyRRs,     "(tmathRRRRtTrueRtFalseRR RRRR(((sJ/woldlab/castor/data00/home/georgi/erange-4.0a/cistematic/cisstat/score.pyt s