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stuart
Commits
7f522196
Commit
7f522196
authored
Jun 23, 2021
by
Marie Bourdon
Browse files
mark_prop chisq backcross
parent
c5d45686
Changes
2
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R/mark_prop.R
View file @
7f522196
...
...
@@ -15,9 +15,6 @@
#### mark_prop ####
## excludes markers depending on proportions of homo/hetorozygous
mark_prop
<-
function
(
tab
,
cross
,
homo
=
NA
,
hetero
=
NA
,
pval
=
NA
,
na
=
0.5
){
#stock colnames to join
names
<-
colnames
(
tab
)
#calculate total number of individuals genotyped for each marker
tab
<-
tab
%>%
mutate
(
n_geno
=
(
n_HM1
+
n_HM2
+
n_HT
))
...
...
@@ -42,6 +39,9 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
mutate
(
exclude_prop
=
case_when
(
p_NA
>
na
~
1
,
T
~
0
))
#stock colnames to join
names
<-
colnames
(
tab
)
#exclude with prop of homo/hetero
if
(
is.na
(
pval
)
==
TRUE
){
#calculate proportion of each genotype
...
...
@@ -56,19 +56,33 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
cross
==
"N2"
&
(
p_HM1
<
homo
|
p_HT
<
hetero
)
~
1
,
T
~
exclude_prop
))
}
#exclude with pval chisq.test
## NEED TO ADD THIS FILTER IF CROSS = N2
if
(
is.na
(
pval
)
==
FALSE
){
}
else
if
(
is.na
(
pval
)
==
FALSE
){
#if cross F2
if
(
cross
==
"F2"
){
tab
<-
tab
%>%
filter
(
p_NA
!=
1
)
%>%
rowwise
()
%>%
mutate
(
.
,
chi_pval
=
tibble
(
n_HM1
,
n_HM2
,
n_HT
)
%>%
chisq.test
(
p
=
c
(
0.25
,
0.25
,
0.5
))
%>%
.
$
p.value
)
%>%
full_join
(
.
,
tab
,
by
=
all_of
(
names
))
tab
<-
tab
%>%
mutate
(
exclude_prop
=
case_when
(
chi_pval
<
pval
~
1
,
T
~
exclude_prop
))
#if cross N2
}
else
if
(
cross
==
"N2"
){
tab
<-
tab
%>%
filter
(
p_NA
!=
1
)
%>%
rowwise
()
%>%
mutate
(
.
,
chi_pval
=
tibble
(
n_HM1
,
n_HT
)
%>%
chisq.test
(
p
=
c
(
0.5
,
0.5
))
%>%
.
$
p.value
)
%>%
full_join
(
.
,
tab
,
by
=
all_of
(
names
))
tab
<-
tab
%>%
mutate
(
exclude_prop
=
case_when
(
chi_pval
<
pval
~
1
,
T
~
exclude_prop
))
}
tab
<-
tab
%>%
filter
(
p_NA
!=
1
)
%>%
rowwise
()
%>%
mutate
(
.
,
chi_pval
=
tibble
(
n_HM1
,
n_HM2
,
n_HT
)
%>%
chisq.test
(
p
=
c
(
0.25
,
0.25
,
0.5
))
%>%
.
$
p.value
)
%>%
full_join
(
.
,
tab
,
by
=
all_of
(
names
))
tab
<-
tab
%>%
mutate
(
exclude_prop
=
case_when
(
chi_pval
<
pval
~
1
,
T
~
exclude_prop
))
}
tab
<-
tab
%>%
select
(
all_of
(
names
),
exclude_prop
)
tab
<-
tab
%>%
select
(
all_of
(
names
))
%>%
select
(
-
c
(
n_geno
,
p_NA
))
return
(
tab
)
}
vignettes/stuaRt.Rmd
View file @
7f522196
...
...
@@ -15,6 +15,8 @@ knitr::opts_chunk$set(
)
```
# stuart
Marie Bourdon
June 2021
...
...
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