External Email - Use Caution
Hi Matthew,
Remember, keep it on the list so that people know the status of the request.
I couldn't get this to work with the "_source_info_" variable. It
seems to be unreadable as a variable name. So, this _may_ be what you
want. I don't know if it can be done with "merge" and I don't know the
function "full_join".
WRKY8_colamp_a<-as.character(
c("AT1G02920","AT1G06135","AT1G07160","AT1G11925","AT1G14540","AT1G16150",
"AT1G21120","AT1G26380","AT1G26410","AT1G35210","AT1G49000","AT1G51920",
"AT1G56250","AT1G66090","AT1G72520","AT1G80840","AT2G02010","AT2G18690",
"AT2G30750","AT2G39200","AT2G43620","AT3G01830","AT3G54150","AT3G55840",
"AT4G03460","AT4G11470","AT4G11890","AT4G14370","AT4G15417","AT4G15975",
"AT4G31940","AT4G35180","AT5G01540","AT5G05300","AT5G11140","AT5G24110",
"AT5G25250","AT5G36925","AT5G46295","AT5G64750","AT5G64905","AT5G66020"))
bHLH10_col_a<-as.character(c("AT1G72520","AT3G55840","AT5G20230","AT5G64750"))
bHLH10_colamp_a<-as.character(
c("AT1G01560","AT1G02920","AT1G16420","AT1G17147","AT1G35210","AT1G51620",
"AT1G57630","AT1G72520","AT2G18690","AT2G19190","AT2G40180","AT2G44370",
"AT3G23250","AT3G55840","AT4G03460","AT4G04480","AT4G04540","AT4G08555",
"AT4G11470","AT4G11890","AT4G16820","AT4G23280","AT4G35180","AT5G01540",
"AT5G05300","AT5G20230","AT5G22530","AT5G24110","AT5G56960","AT5G57010",
"AT5G57220","AT5G64750","AT5G66020"))
# let myenter be the sorted superset
myenter<-
sort(unique(c(WRKY8_colamp_a,bHLH10_col_a,bHLH10_colamp_a)))
splice<-function(x,y) {
nx<-length(x)
ny<-length(y)
newy<-rep(NA,nx)
if(ny) {
yi<-1
for(xi in 1:nx) {
if(x[xi] == y[yi]) {
newy[xi]<-y[yi]
yi<-yi+1
}
if(yi>ny) break()
}
}
return(newy)
}
comatgs<-list(WRKY8_colamp_a=WRKY8_colamp_a,
bHLH10_col_a=bHLH10_col_a,bHLH10_colamp_a=bHLH10_colamp_a)
mydf3<-data.frame(myenter,stringsAsFactors=FALSE)
for(j in 1:length(comatgs)) {
tmp<-data.frame(splice(myenter,sort(comatgs[[j]])))
names(tmp)<-names(comatgs)[j]
mydf3<-cbind(mydf3,tmp)
}
Jim
On Fri, Mar 22, 2019 at 10:29 AM Matthew
<mccorm...@molbio.mgh.harvard.edu> wrote:
Hi Jim,
Thanks for the reply. That was pretty dumb of me. I took that out of the
loop.
comatgs is longer than this but here is a sample of 4 of 569 elements:
$WRKY8_colamp_a
[1] "AT1G02920" "AT1G06135" "AT1G07160" "AT1G11925" "AT1G14540" "AT1G16150"
"AT1G21120"
[8] "AT1G26380" "AT1G26410" "AT1G35210" "AT1G49000" "AT1G51920" "AT1G56250"
"AT1G66090"
[15] "AT1G72520" "AT1G80840" "AT2G02010" "AT2G18690" "AT2G30750" "AT2G39200"
"AT2G43620"
[22] "AT3G01830" "AT3G54150" "AT3G55840" "AT4G03460" "AT4G11470" "AT4G11890"
"AT4G14370"
[29] "AT4G15417" "AT4G15975" "AT4G31940" "AT4G35180" "AT5G01540" "AT5G05300"
"AT5G11140"
[36] "AT5G24110" "AT5G25250" "AT5G36925" "AT5G46295" "AT5G64750" "AT5G64905"
"AT5G66020"
$`_source_info_`
character(0)
$bHLH10_col_a
[1] "AT1G72520" "AT3G55840" "AT5G20230" "AT5G64750"
$bHLH10_colamp_a
[1] "AT1G01560" "AT1G02920" "AT1G16420" "AT1G17147" "AT1G35210" "AT1G51620"
"AT1G57630"
[8] "AT1G72520" "AT2G18690" "AT2G19190" "AT2G40180" "AT2G44370" "AT3G23250"
"AT3G55840"
[15] "AT4G03460" "AT4G04480" "AT4G04540" "AT4G08555" "AT4G11470" "AT4G11890"
"AT4G16820"
[22] "AT4G23280" "AT4G35180" "AT5G01540" "AT5G05300" "AT5G20230" "AT5G22530"
"AT5G24110"
[29] "AT5G56960" "AT5G57010" "AT5G57220" "AT5G64750" "AT5G66020"
I have been thinking of something like this:
lenmyen <- length(myenter) # get length of longest list
length(comatgs[[j]) <- lenmyen # make each list length of
myenter
atglsts <- as.data.frame(comatgs[j]) # create dataframe
colnames(atglsts) <- "AGI" # rename column to 'AGI'
mydf3 <- full_join(mydf3, atglsts, by = "AGI" # full_join
Matthew
On 3/21/2019 7:12 PM, Jim Lemon wrote:
External Email - Use Caution
Hi Matthew,
First thing, don't put:
mydf3 <- data.frame(myenter)
inside your loop, otherwise you will reset the value of mydf3 each
time and end up with only "myenter" and the final list. Without some
idea of the contents of comatgs, it is difficult to suggest a way to
get what you want.
Jim
On Fri, Mar 22, 2019 at 8:16 AM Matthew
<mccorm...@molbio.mgh.harvard.edu> wrote:
My apologies, my first e-mail formatted very poorly when sent, so I am
trying again with something I hope will be less confusing.
I have been trying create a dataframe by looping through a list of lists,
and using dplyr's full_join so as to keep common elements on the same row.
But, I have a couple of problems.
1) The lists have different numbers of elements.
2) In the final dataframe, I would like the column names to be the names
of the lists.
Is it possible ?
Code: *for(j in avector){****mydf3 <- data.frame(myenter) ****atglsts <-
as.data.frame(comatgs[j]) ****mydf3 <- full_join(mydf3, atglsts) ****}*
Explanation: # Start out with a list, myenter, to dataframe. mydf3 now
has 1 column. # This first column will be the longest column in the
final mydf3. # Loop through a list of lists, comatgs, and with each loop
a particular list # is made into a dataframe of one column, atglsts. #
The name of the column is the name of the list. # Each atglsts dataframe
has a different number of elements. # What I want to do, is to add the
newly made dataframe, atglsts, as a # new column of the data frame,
mydf3 using full_join # in order to keep common elements on the same
row. # I could rename the colname to 'AGI' so that I can join by 'AGI',
# but then I would lose the name of the list. # In the final dataframe,
I want to know the name of the original list # the column was made from. Matthew
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