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7a750efa
Commit
7a750efa
authored
Mar 13, 2019
by
Eric Coissac
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Patch the extract.obiclean function
parent
c09e222c
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8 changed files
with
35 additions
and
31 deletions
+35
-31
DESCRIPTION
DESCRIPTION
+1
-1
obiclean.R
R/obiclean.R
+22
-20
extrapol.freq.Rd
man/extrapol.freq.Rd
+2
-2
initialize-methods.Rd
man/initialize-methods.Rd
+2
-1
m.univariate.test.Rd
man/m.univariate.test.Rd
+2
-1
map.extrapol.freq.Rd
man/map.extrapol.freq.Rd
+2
-2
plot.PCRplate.Rd
man/plot.PCRplate.Rd
+2
-2
threshold-mask-methods.Rd
man/threshold-mask-methods.Rd
+2
-2
No files found.
DESCRIPTION
View file @
7a750efa
...
...
@@ -35,4 +35,4 @@ Collate:
'taxoDBtree.R'
'taxonomic.resolution.R'
'taxonomy_classic_table.R'
RoxygenNote: 6.
0
.1
RoxygenNote: 6.
1
.1
R/obiclean.R
View file @
7a750efa
...
...
@@ -56,9 +56,8 @@ setMethod("extracts.obiclean", "metabarcoding.data", function(obj) {
cols
=
colnames
(
obj
@
motus
)
cleancols
=
grep
(
pat
,
cols
)
clean.names
=
cols
[
cleancols
]
p
=
grep
(
pat
,
cols
)
d
=
t
(
as.factor.or.matrix
(
obj
@
motus
[,
p
]))
n
=
sapply
(
strsplit
(
cols
[
p
],
':'
),
function
(
y
)
y
[[
2
]])
d
=
t
(
as.factor.or.matrix
(
obj
@
motus
[,
cleancols
]))
n
=
sapply
(
strsplit
(
cols
[
cleancols
],
':'
),
function
(
y
)
y
[[
2
]])
rownames
(
d
)
=
n
d
=
d
[
rownames
(
obj
@
reads
),]
obj
[[
"obiclean_status"
]]
=
d
...
...
@@ -68,28 +67,31 @@ setMethod("extracts.obiclean", "metabarcoding.data", function(obj) {
pat
=
"^obiclean_count:.*$"
cols
=
colnames
(
newmotus
)
cleancols
=
grep
(
pat
,
cols
)
clean.names
=
cols
[
cleancols
]
p
=
grep
(
pat
,
cols
)
d
=
t
(
as.factor.or.matrix
(
newmotus
[,
p
]))
n
=
sapply
(
strsplit
(
cols
[
p
],
':'
),
function
(
y
)
y
[[
2
]])
rownames
(
d
)
=
n
d
=
d
[
rownames
(
obj
@
reads
),]
obj
[[
"obiclean_count"
]]
=
d
newmotus
=
newmotus
[
-
cleancols
]
if
(
length
(
cleancols
)
>
0
)
{
clean.names
=
cols
[
cleancols
]
d
=
t
(
as.factor.or.matrix
(
newmotus
[,
cleancols
]))
n
=
sapply
(
strsplit
(
cols
[
cleancols
],
':'
),
function
(
y
)
y
[[
2
]])
rownames
(
d
)
=
n
d
=
d
[
rownames
(
obj
@
reads
),]
obj
[[
"obiclean_count"
]]
=
d
newmotus
=
newmotus
[
-
cleancols
]
}
pat
=
"^obiclean_cluster:.*$"
cols
=
colnames
(
newmotus
)
cleancols
=
grep
(
pat
,
cols
)
clean.names
=
cols
[
cleancols
]
p
=
grep
(
pat
,
cols
)
d
=
t
(
as.factor.or.matrix
(
newmotus
[,
p
]))
n
=
sapply
(
strsplit
(
cols
[
p
],
':'
),
function
(
y
)
y
[[
2
]])
rownames
(
d
)
=
n
d
=
d
[
rownames
(
obj
@
reads
),]
obj
[[
"obiclean_cluster"
]]
=
d
newmotus
=
newmotus
[
-
cleancols
]
if
(
length
(
cleancols
)
>
0
)
{
clean.names
=
cols
[
cleancols
]
d
=
t
(
as.factor.or.matrix
(
newmotus
[,
cleancols
]))
n
=
sapply
(
strsplit
(
cols
[
cleancols
],
':'
),
function
(
y
)
y
[[
2
]])
rownames
(
d
)
=
n
d
=
d
[
rownames
(
obj
@
reads
),]
obj
[[
"obiclean_cluster"
]]
=
d
newmotus
=
newmotus
[
-
cleancols
]
}
newdata
=
copy.metabarcoding.data
(
obj
,
motus
=
newmotus
)
...
...
man/extrapol.freq.Rd
View file @
7a750efa
...
...
@@ -4,8 +4,8 @@
\alias{extrapol.freq}
\title{Read frequencies krigging}
\usage{
extrapol.freq(x, min.coord, max.coord, grid.grain = 100, coords,
otus.table,
cutoff = 0.001, return.metabarcoding.data = FALSE)
extrapol.freq(x, min.coord, max.coord, grid.grain = 100, coords,
otus.table,
cutoff = 0.001, return.metabarcoding.data = FALSE)
}
\arguments{
\item{x}{a vector or matrix from a row-normalized read table
...
...
man/initialize-methods.Rd
View file @
7a750efa
...
...
@@ -7,7 +7,8 @@
\title{metabarcoding.data constructor}
\usage{
\S4method{initialize}{metabarcoding.data}(.Object, reads, samples, motus,
taxonomy = NULL, taxid = NULL, sample.margin = NA, layers = list())
taxonomy = NULL, taxid = NULL, sample.margin = NA,
layers = list())
}
\description{
metabarcoding.data constructor
...
...
man/m.univariate.test.Rd
View file @
7a750efa
...
...
@@ -4,7 +4,8 @@
\alias{m.univariate.test}
\title{Test the significance of the M statistics by Monte-Carlo}
\usage{
m.univariate.test(w, groups, resampling = 100, alternative = "two.sided")
m.univariate.test(w, groups, resampling = 100,
alternative = "two.sided")
}
\arguments{
\item{w}{the weigth matrix indicating the presence probability of each motu
...
...
man/map.extrapol.freq.Rd
View file @
7a750efa
...
...
@@ -4,8 +4,8 @@
\alias{map.extrapol.freq}
\title{Maps of krigged log10-transformed frequencies}
\usage{
map.extrapol.freq(x, path = NULL, col.name = NULL, index,
cutoff = 0.001,
add.points = NULL, adj = 4)
map.extrapol.freq(x, path = NULL, col.name = NULL, index,
cutoff = 0.001,
add.points = NULL, adj = 4)
}
\arguments{
\item{x}{an extrapol.freq output}
...
...
man/plot.PCRplate.Rd
View file @
7a750efa
...
...
@@ -4,8 +4,8 @@
\alias{plot.PCRplate}
\title{Plot PCR plates}
\usage{
\method{plot}{PCRplate}(x, samples = NULL, col = "cyan2",
different = T,
...)
\method{plot}{PCRplate}(x, samples = NULL, col = "cyan2",
different = T,
...)
}
\arguments{
\item{x}{a \code{\link{metabarcoding.data}} object}
...
...
man/threshold-mask-methods.Rd
View file @
7a750efa
...
...
@@ -6,8 +6,8 @@
\alias{threshold.mask-methods,metabarcoding.data}
\title{Computes a cumulatif thresold mask for filtering read aboundancies.}
\usage{
\S4method{threshold.mask}{metabarcoding.data}(data, MARGIN,
threshold = 0.97,
operator = "<")
\S4method{threshold.mask}{metabarcoding.data}(data, MARGIN,
threshold = 0.97,
operator = "<")
}
\arguments{
\item{data}{The \code{\linkS4class{metabarcoding.data}} instance
...
...
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