Returns an S3 object of class
npartbl which is basically
a compact version of MERLIN's
Character vector containing the
--tabulate option is used to output convenient tables
summarising linkage analysis results in two files per chromosome:
nonparametric.tbl file will be output if MERLIN is run with
at least one of the options
These compute a LOD score using the Kong and Cox linear model, which is found
in the 'lod' column. The two options are
designated in the 'analysis' column of the file by character strings containing
'ALL' and 'pairs', respectively.
--exp option is also specified,
an additional LOD score is calculated using the
Kong and Cox exponential mode. This is found in the 'exlod' column.
If the family consists of a single affected sibpair, the 'ALL' and 'pairs' statistics will be identical. The 'pairs' statistic also considers sharing within inbred individuals. For more information, see MERLIN's website: http://csg.sph.umich.edu/abecasis/merlin/index.html
S3 object of class
npartbl, which is
a list with:
npartbl: data.frame with 4 or 5* columns (chr, pos, analysis, lod, exlod*)
max_lods: data.frame with 3 columns (chr, max_lod, max_hlod)
n_markers: data.frame with 2 columns (chr, n)
merlin_options: character vector of length 3, indicating the options inferred to have been supplied to MERLIN for the nonparametric linkage analysis
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