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commit 35dd40f6e2a0e2744105dbc03e29abe29f0c9f3c Author: Andreas Tille <[email protected]> Date: Tue Jul 19 10:57:39 2016 +0200 Add at least one manpage where the executable does some sensible printout. Install examples --- debian/changelog | 2 ++ debian/copyright | 1 + debian/examples | 3 +++ debian/manpages | 1 + debian/mans/smarteigenstrat.1 | 34 ++++++++++++++++++++++++++++++++++ 5 files changed, 41 insertions(+) diff --git a/debian/changelog b/debian/changelog index 4483761..bbbe8ee 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,8 @@ eigensoft (6.1.2+dfsg-1) UNRELEASED; urgency=medium * cme fix dpkg-control * hardening=+bindnow * Leave only wrapper scripts in /usr/bin, executables go to /usr/lib/eigensoft + * add at least one manpage + * add examples [ Tatiana Malygina ] * Fix headers diff --git a/debian/copyright b/debian/copyright index dd58f4e..684d11d 100644 --- a/debian/copyright +++ b/debian/copyright @@ -16,6 +16,7 @@ Files-Excluded: bin/baseprog */*.o */*.a */.*.swp + */lsqproject.pdf Files: * Copyright: 2010-2016 Alkes Price <[email protected]>, diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..4725453 --- /dev/null +++ b/debian/examples @@ -0,0 +1,3 @@ +CONVERTF +EIGENSTRAT +POPGEN diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..63ab24a --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/mans/* diff --git a/debian/mans/smarteigenstrat.1 b/debian/mans/smarteigenstrat.1 new file mode 100644 index 0000000..f62372f --- /dev/null +++ b/debian/mans/smarteigenstrat.1 @@ -0,0 +1,34 @@ +.TH SMARTEIGENSTRAT "1" "July 2016" "smarteigenstrat 6.1.2" "User Commands" +.SH NAME +smarteigenstrat \- reduction of population bias for genetic analyses +.SH SYNOPSIS +.B smarteigenstrat +\fB\-i\fR <genotypefile> \fB\-a\fR <indivfile> \fB\-b\fR <snpfile> \fB\-p\fR <pcafile> \fB\-o\fR <outputfile> \fB\-l\fR <logfile> \fB\-k\fR <numpca> \fB\-q\fR <qtlmode> +.SH DESCRIPTION +The program \fBsmarteigenstrat\fR is part of EIGENSOFT. +.P +The EIGENSOFT package combines functionality from the group's population +genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification +method (Price et al. 2006). The EIGENSTRAT method uses principal components +analysis to explicitly model ancestry differences between cases and +controls along continuous axes of variation; the resulting correction is +specific to a candidate marker's variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to +detect true associations. The EIGENSOFT package has a built-in plotting +script and supports multiple file formats and quantitative phenotypes. +.SH OPTIONS +.TP +\fB\-i\fR +genotype file (PED, PACKEDPED, EIGENSTRAT, ANCESTRYMAP or PACKEDANCESTRYMAP format)\-o output file (chisq) +.TP +\fB\-l\fR +logfile (screen output,including error messages) +.TP +\fB\-q\fR +YES for quantitative phenotype or NO otherwise +.PP +For quantitative phenotype, sixth column of .ped file or third column of EIGENSTRAT .ind file +should be real numbers. For non\-quantitative phenotype, sixth column of .ped or third column +should be 'Case' or 'Control' +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/eigensoft.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
