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Statistical-Genetics
RAISS
Commits
cd04d3fd
Commit
cd04d3fd
authored
Mar 28, 2018
by
Hanna JULIENNE
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impute_jass/impute_jass/ld_matrix.py
impute_jass/impute_jass/ld_matrix.py
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impute_jass/impute_jass/ld_matrix.py
View file @
cd04d3fd
...
...
@@ -49,7 +49,6 @@ def generate_sparse_matrix(plink_ld, ref_chr_df):
mat_ld
=
pd
.
DataFrame
(
sym
,
index
=
mat_ld
.
index
,
columns
=
mat_ld
.
columns
)
re_index
=
ref_chr_df
.
loc
[
mat_ld
.
index
].
sort_values
(
by
=
"pos"
).
index
mat_ld
=
mat_ld
.
loc
[
re_index
,
re_index
]
# mat_ld = pd.DataFrame(np.maximum(mat_ld.values, mat_ld.values.transpose()), index=un_index, columns=un_index)
mat_ld
=
mat_ld
.
to_sparse
()
return
mat_ld
#mat_ld.to_pickle(path_ld_mat,, compression='gzip')
...
...
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