obitools/ROBITools
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Patch the extract.obiclean function

Browse Source
This commit is contained in:
Eric Coissac
2019-03-13 23:09:46 +01:00
parent c09e222c58
commit 7a750efaeb
8 changed files with 35 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
R/obiclean.R
View File

@@ -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)