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(`*` BB)H`?@(``?@ (`*`D* FD*`" 9(`* F.#PB㿐. .`@D..@ J`?`?@H`?@@@@@`?@`?27`?";7X Bc`㿈?*chD7+3cpD1cx -#c 5 Hc3c1#Dc3c13 V#1FVcܥ VcT V#ȍνV@ Vڡ VRHL3chcDJ1#@1#c3c1 D#c3c1@3 T 1ڡT`֍T`3L T 1ޥT` ؝T`(3P T 01 HƵT`8\ T`@ҙ TNT TZTH3cpF㿐/K@ ???㿐㿠K㿠 Usage: prest pedfile chromfiles 1 (or 2) r Unable to open pedfile: %s wprest_out1prest_out2prest_out3prest_errors%d %d %d %d %d %d Invalid %d_th line in pedfile: %s Correct format is: pedid id f_id m_id sex affect_status Warning: The length of the lines in file %s is too long (>5000). Adjust MAXSTR and recompile. %d%d %d %d %dpedigree id = %d being used twice %s %s Unable to open marker_file %s Unable to open genotype_file %s Invalid line in chromfiles: %s %s Correct format is: marker_file genotype_file%d %d%lfError of marker spacing in file %s: %d markers, should be (%d - 1) spacings Error in marker data Prest has detected Mendelian errors# Number of pedigrees: %d # Total number of individuals: # Number of chromosomes: # Total number of markers: # Number of markers on each chromosome %s: %5d # Number of genotyped pairs found in each of the # relationship categories analyzed by PREST: # (Note that unrelated pairs are checked within each pedigree.) Total: %d %7d full-sib pairs %7d half-sib pairs %7d grandparent-grandchild pairs %7d avuncular pairs %7d first-cousin pairs %7d unrelated pairs %7d half-avuncular pairs %7d half-first-cousin pairs %7d half-sib-plus-first-cousin pairs %7d parent-offspring pairs # Summary of genotyped pairs found in each pedigree pedid size f.sib h.sib g.p.c avun. f.cous. unrel. h.avun h.f.cous. h.sib+f.cous. p.o. Total %8d %4d %4d %8d # Assuming that there are not many misclassified relative pairs in the # data set and assuming that all the pairs are typed on roughly the # same markers (because which markers are typed affects the null means # of the AIBS and IBS statistics and affects the null variances of the # EIBD, AIBS and IBS statistics), then the sample averaged observed # statistics for each relationship type should not be significantly # different from what is expected. If they are significantly # different, if may indicate that the allele frequencies are not # accurately estimated, or that the assumptions of population # homogeneity and Hardy-Weinberg equilibrium are not appropriate. # It could also indicate a problem with the way the data are coded # (see item #7 in 'Tips' file). The following output contains # the information of sample summary of the statistics # obs = sample averaged observed statistic # mu(std) = sample averaged null mean (sample std. dev. of null mean) # (Note that the null mean of EIBD depends only on the null relationship, not on the data, so for EIBD # we give the null mean in place of the sample averaged null mean # std(std) = sample averaged standard deviation # (sample std. dev. of null standard deviation) # no.mark = sample averaged number of typed markers for a pair # (sample std. dev.) no.pairs no.mark(std) full-sib %7d NA( NA) half-sib %7d NA( NA) grandp-c %7d NA( NA) avuncular %7d NA( NA) f-cousin %7d NA( NA) unrelated %7d NA( NA) h-avuncular %7d NA( NA) h-f-cousin %7d NA( NA) h-sib+f-cous %7d NA( NA) pa-offspring %7d NA( NA) # Sample summary of EIBD obs mu std( std) full-sib %6.4f %6.4f %6.4f(%8.6f) half-sib %6.4f %6.4f %6.4f(%8.6f) grandp-c %6.4f %6.4f %6.4f(%8.6f) avuncular %6.4f %6.4f %6.4f(%8.6f) f-cousin %6.4f %6.4f %6.4f(%8.6f) unrelated NA NA NA( NA) h-avuncular %6.4f %6.4f %6.4f(%8.6f) h-f-cousin %6.4f %6.4f %6.4f(%8.6f) h-sib+f-cousin %6.4f %6.4f %6.4f(%8.6f) pa-offspring NA NA NA( NA) # Sample summary of AIBS obs mu( std) std( std) full-sib %6.4f %6.4f(%8.6f) %6.4f(%8.6f) half-sib %6.4f %6.4f(%8.6f) %6.4f(%8.6f) grandp-c %6.4f %6.4f(%8.6f) %6.4f(%8.6f) avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) unrelated NA NA( NA) NA( NA) h-avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-sib+f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) pa-offspring %6.4f %6.4f(%8.6f) %6.4f(%8.6f) # Sample summary of IBS unrelated %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) pa-offspring %6.4f %6.4f(%8.6f) %6.4f(%8.6f) pa-offspring %6.4f %6.4f( NA) %6.4f( NA) pa-offsprin NA NA( NA) NA( NA) h-sib+f-cousin %6.4f %6.4f( NA) %6.4f( NA) h-sib+f-cousin NA NA( NA) NA( NA) h-f-cousin %6.4f %6.4f( NA) %6.4f( NA) h-f-cousin NA NA( NA) NA( NA) h-avuncular %6.4f %6.4f( NA) %6.4f( NA) h-avuncular NA NA( NA) NA( NA) unrelated %6.4f %6.4f( NA) %6.4f( NA) f -cousin %6.4f %6.4f( NA) %6.4f( NA) f-cousin NA NA( NA) NA( NA) avuncular %6.4f %6.4f( NA) %6.4f( NA) avuncular NA NA( NA) NA( NA) grandp-c %6.4f %6.4f( NA) %6.4f( NA) grandp-c NA NA( NA) NA( NA) half-sib %6.4f %6.4f( NA) %6.4f( NA) half-sib NA NA( NA) NA( NA) full-sib %6.4f %6.4f( NA) %6.4f( NA) full-sib NA NA( NA) NA( NA) pa-offspring %6.4f %6.4f( NA) %6.4f( NA) pa-offsprin NA NA NA( NA) NA( NA) h-avuncular %6.4f %6.4f( NA) %6.4f( NA) f-cousin %6.4f %6.4f( NA) %6.4f( NA) h-sib+f-cousin %6.4f %6.4f %6.4f( NA) h-sib+f-cousin NA NA NA( NA) h-f-cousin %6.4f %6.4f %6.4f( NA) h-f-cousin NA NA NA( NA) h-avuncular %6.4f %6.4f %6.4f( NA) h-avuncular NA NA NA( NA) f-cousin %6.4f %6.4f %6.4f( NA) f-cousin NA NA NA( NA) avuncular %6.4f %6.4f %6.4f( NA) avuncular NA NA NA( NA) grandp-c %6.4f %6.4f %6.4f( NA) grandp-c NA NA NA( NA) half-sib %6.4f %6.4f %6.4f( NA) half-sib NA NA NA( NA) full-sib %6.4f %6.4f %6.4f( NA) full-sib NA NA NA( NA) pa-offspring %7d %6.1f(%6.1f) h-sib+f-cous %7d %6.1f(%6.1f) h-f-cousin %7d %6.1f(%6.1f) h-avuncular %7d %6.1f(%6.1f) unrelated %7d %6.1f(%6.1f) f-cousin %7d %6.1f(%6.1f) avuncular %7d %6.1f(%6.1f) grandp-c %7d %6.1f(%6.1f) half-sib %7d %6.1f(%6.1f) full-sib %7d %6.1f(%6.1f) # Number of pairs checked by MLRT %7d half-sib pairs In each pedigree # Number of pairs that have p-value of either EIBD or AIBS less than 0.2 # (for unrelated, p-value of IBS less than 0.2). # This is the number of pairs for which PREST would perform the MLRT. # (The MLRT will actually be performed only if option 2 is chosen.) # For each pair, performance of the MLRT, including 100,000 # simulated realizations takes approximately 5 minutes on # a Sun Ultra II with 360-MHz processor. which are reported in the file prest_errors. In the current implementation of prest, the presence of Mendelian errors is not taken into account in the hypothesis testing.%%%dd %%%dd %%%dd %%2d %%%dd NA %6.4f %6.4f %6.4f NA %7.5f %7.5f pedigree %d done NA %8.6f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f %7.5f %7.5f %7.5f NA %6.4f %6.4f %6.4f NA NA %7.5f Check prest_errors file, and re-run the program Spacing cannot be negative value Spacing between adjacent markers should be in recombination fraction (theta), not in centi-Morgan Error in %s's %d_th marker sum of allele freq. = %f Error of allele freq. in %d_th marker in file %s (<=0 or > 1): Error of allele freq. in %d_th marker in file %s: Error in file %s: %s Error reading num_mark from file %s %s Error in the pedigrees Check file prest_errors file, and re-run the program Incorrect input: %s Usage: prest pedfile chromfiles 1 (or 2) use 1, if you only want to apply EIBD, AIBS, IBS use 2, if you also want to apply MLRT Unable to open output file: prest_errors Unable to open output file: prest_out3 Unable to open output file: prest_out2 Unable to open output file: prest_out1 Unable to open chromfiles: %s use 1 if apply only EIBD, AIBS, IBS test statistics use 2 if further apply MLRT test example: prest pedfile chromfiles 1 ??zG{?6C-@$?ə???ffffff@j@jerrors in pedigree %d: pedigree %d is not complete: %d's parents: %d and/or %d do not have their parent's ids %d has two genders individual id = %d being used %d'th parents have the same id Warning: The length of the %d_th line in file %s Genotyping errors: pedigree %d, at %s's %dth marker %d's genotypy is %d %d no. of alleles of this marker is %d Error reading genotype data for %d in ped %d at %s Error reading genotype data for %d in ped %d at %s at line %d Mendelian errors: pedigree %d at %s's %dth marker %d's parents are %d %d, and genotype: %d %d %d %d %d %d %d's parents are %d %d, and genotype: ?@@@@@@@?UUUUUU?UUUUUU?@@@@@@@?UUUUUU?UUUUUU?@Y?zG{???zG{?ə?333333@@ >?\>?`d@?program is wrong for EIBD@@ ?@?PbM?@? \:%?Q!?uKOOq?/Y?|5/?F.Jc֦?Vȝ(?J 7?`$DV?z0??`d@@?`d@@??ə@j@Y?@@ ?@?? \:%?Q!?uKOOq?/Y?|5/?F.Jc֦?Vȝ(?J 7?`$DV?z0?