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Statistical-Genetics
RAISS
Commits
63689893
Commit
63689893
authored
Mar 07, 2018
by
Hanna JULIENNE
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add option to the centered windows function
parent
c79adc67
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1
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1 changed file
with
9 additions
and
7 deletions
+9
-7
impute_jass/impute_jass/windows.py
impute_jass/impute_jass/windows.py
+9
-7
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impute_jass/impute_jass/windows.py
View file @
63689893
...
...
@@ -54,7 +54,7 @@ def prepare_Zscore_for_imputation(ref_panel, Zscores):
def
in_region
(
pos_vector
,
start
,
end
):
return
((
start
<
pos_vector
)
&
(
pos_vector
<
end
))
def
centered_window_imputation
(
LD_file
,
ref_panel_folder
,
Z
file
,
window_size
):
def
centered_window_imputation
(
LD_file
,
ref_panel_folder
,
Z
scores
,
window_size
,
unknowns
=
pd
.
Series
([])
):
"""
Each missing Snp is imputed by known snp found in a window centered on the SNP to impute
Argument
...
...
@@ -66,11 +66,13 @@ def centered_window_imputation(LD_file, ref_panel_folder, Zfile, window_size):
LD_mat
=
generate_sparse_matrix
(
LD_file
,
ref_panel
)
Zscores
=
pd
.
read_csv
(
Zfile
,
index_col
=
0
,
sep
=
"
\t
"
)
#
Zscores = pd.read_csv(Zfile, index_col=0, sep="\t")
Zscores
=
prepare_Zscore_for_imputation
(
ref_panel
,
Zscores
)
# Find Snp to impute
unknowns
=
LD_mat
.
index
.
difference
(
Zscores
.
index
)
if
len
(
unknowns
)
==
0
:
unknowns
=
LD_mat
.
index
.
difference
(
Zscores
.
index
)
N_snp
=
len
(
unknowns
)
print
(
"### Imputation of {0} snps ###"
.
format
(
len
(
unknowns
)))
i
=
0
...
...
@@ -85,20 +87,20 @@ def centered_window_imputation(LD_file, ref_panel_folder, Zfile, window_size):
in_LD_reg_n_window
=
in_region
(
Zscores
.
pos
,
int
(
start_ld_block
),
int
(
end_ld_block
))
&
in_region
(
Zscores
.
pos
,
start_pos
,
end_pos
)
known
=
Zscores
.
loc
[
in_LD_reg_n_window
].
index
Sig_t
=
LD_mat
.
loc
[
known
,
known
]
Sig_i_t
=
LD_mat
.
loc
[
snp_unknown
,
known
]
Zt
=
Zscores
.
loc
[
known
,
'Z'
]
if
(
len
(
known
)
>
0
):
imp
=
ImpG_model_snp
(
Zt
,
Sig_t
,
Sig_i_t
)
Zscores
.
loc
[
snp_unknown
,
[
"pos"
,
"A0"
,
"A1"
]]
=
ref_panel
.
loc
[
snp_unknown
,
[
'pos'
,
"Ref_all"
,
"alt_all"
]]
Zscores
.
loc
[
snp_unknown
,
"Z"
]
=
imp
[
'mu'
]
Zscores
.
loc
[
snp_unknown
,
"Var"
]
=
imp
[
'Var'
]
Zscores
[
snp_unknown
,
'Nsnp_to_impute'
]
=
len
(
known
)
Zscores
.
loc
[
snp_unknown
,
'Nsnp_to_impute'
]
=
len
(
known
)
i
=
i
+
1
if
i
%
10
==
0
:
if
i
%
10
0
==
0
:
print
(
"{0}\%"
.
format
(
np
.
round
(
i
/
N_snp
,
4
)))
return
Z
t
.
sort_values
(
by
=
"pos"
)
return
Z
scores
.
sort_values
(
by
=
"pos"
)
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