I have a question how to extract parts of the text and convert them df output.
This is an example of my df, output of one row in my one column (content of one cell)
[{"id"=>"aaaaaaaaaaaaaaaa", "effortDate"=>"2021-07-04T23:00:00.000Z", "effort"=>2, "author"=>"a:aa:a"}, {"id"=>"bbbbbbbbbbbbbb", "effortDate"=>"2021-07-11T23:00:00.000Z", "effort"=>1, "author"=>"b:bb:b"}, {"id"=>"ccccccccccccc", "effortDate"=>"2021-07-17T23:00:00.000Z", "effort"=>1, "author"=>"c:cc:c"}]
My expected output would be to have 2 columns with as many rows I get from this string:
effortDate
2021-07-04
2021-04-11
and second column
effort
2
1
Any suggestion how to achieve that?
Thanks!
looks like json-content... but the => messes with the reading. If you replace it with :, you sould be able to read properly.
mystr <- '[{"id"=>"aaaaaaaaaaaaaaaa", "effortDate"=>"2021-07-04T23:00:00.000Z", "effort"=>2, "author"=>"a:aa:a"}, {"id"=>"bbbbbbbbbbbbbb", "effortDate"=>"2021-07-11T23:00:00.000Z", "effort"=>1, "author"=>"b:bb:b"}, {"id"=>"ccccccccccccc", "effortDate"=>"2021-07-17T23:00:00.000Z", "effort"=>1, "author"=>"c:cc:c"}]'
jsonlite::fromJSON(gsub("=>", ":", mystr))
# id effortDate effort author
# 1 aaaaaaaaaaaaaaaa 2021-07-04T23:00:00.000Z 2 a:aa:a
# 2 bbbbbbbbbbbbbb 2021-07-11T23:00:00.000Z 1 b:bb:b
# 3 ccccccccccccc 2021-07-17T23:00:00.000Z 1 c:cc:c
I have an object (Seurat object) an I need to get certain data out of it
> sc#misc[["colors"]][["seurat_clusters"]]
0 1 2 3 4 5 6 7
"#CC0C00FF" "#5C88DAFF" "#84BD00FF" "#FFCD00FF" "#7C878EFF" "#00B5E2FF" "#00AF66FF" "#CC0C00B2"
This data is needed as an vector but I don't know how to pull "#CC0C00FF" "#5C88DAFF" etc. out of it.
In order to hand this data to the next function, the result should look like this:
> vec
[1] "#CC0C00FF" "#5C88DAFF" "#84BD00FF"
Thanks in advance!
Solved it! I'm pretty disappointed by myself, because I didn't know this function existed:
> as.vector(sc#misc[["colors"]][["seurat_clusters"]])
[1] "#CC0C00FF" "#5C88DAFF" "#84BD00FF" "#FFCD00FF" "#7C878EFF" "#00B5E2FF" "#00AF66FF" "#CC0C00B2"
I have a list which included a mix of data type (character) and data structure (dataframe).
I want to keep only the dataframes and remove the rest.
> head(list)
[[1]]
[1] "/Users/Jane/R/12498798.txt error"
[[2]]
match
1 Japan arrests man for taking gun
2 Extradition bill turns ugly
file
1 /Users/Jane/R/12498770.txt
2 /Users/Jane/R/12498770.txt
[[3]]
[1] "/Users/Jane/R/12498780.txt error"
I expect the final list to contain only dataframes:
[[2]]
match
1 Japan arrests man for taking gun
2 Extradition bill turns ugly
file
1 /Users/Jane/R/12498770.txt
2 /Users/Jane/R/12498770.txt
Based on the example, it is possible that the OP's list elements are vectors and want to remove any element having 'error' substring
list[!sapply(list, function(x) any(grepl("error$", x)))]
I am trying to read a TSV file in R using the read.table function.
myTable <- read.table("file_path", sep='\t', header=T)
But when I try the command
names(myTable)
It gives me column names which are odd numbered, while merging the even numbered columns with those.
[1] "GeneSymbol" "GSM480304_JK_C_05.07.mas5.chp"
[3] "GSM480355_JK_C_05.07.mas5.chp" "GSM480480_JK_C_05.07.mas5.chp"
[5] "GSM480555_JK_C_05.07.mas5.chp" "GSM480634_JK_C_05.07.mas5.chp"
These are exact column names and you can see that two column names are separated by space while only ODD numbered column names are listed.
The output should be like this:
[1] "GeneSymbol"
[2] "GSM480304_JK_C_05.07.mas5.chp"
[3] "GSM480355_JK_C_05.07.mas5.chp"
[4] "GSM480480_JK_C_05.07.mas5.chp"
[5] "GSM480555_JK_C_05.07.mas5.chp"
[6] "GSM480634_JK_C_05.07.mas5.chp"
This is creating problem in assigning names to another table where I want to use these column names. Any suggestions ?
As noted in the comments, R is displaying all the columns, but not in the format you expect. This can be forced by casting the result of names() with as.data.frame() as follows:
rawData <- "
Number,Name,Type1,Type2,Total,HP,Attack,Defense,SpecialAtk,SpecialDef,Speed,Generation,Legendary
1,Bulbasaur,Grass,Poison,318,45,49,49,65,65,45,1,False
2,Ivysaur,Grass,Poison,405,60,62,63,80,80,60,1,False
3,Venusaur,Grass,Poison,525,80,82,83,100,100,80,1,False
3,VenusaurMega Venusaur,Grass,Poison,625,80,100,123,122,120,80,1,False
4,Charmander,Fire,,309,39,52,43,60,50,65,1,False
5,Charmeleon,Fire,,405,58,64,58,80,65,80,1,False
6,Charizard,Fire,Flying,534,78,84,78,109,85,100,1,False
6,CharizardMega Charizard X,Fire,Dragon,634,78,130,111,130,85,100,1,False
6,CharizardMega Charizard Y,Fire,Flying,634,78,104,78,159,115,100,1,False
7,Squirtle,Water,,314,44,48,65,50,64,43,1,False
8,Wartortle,Water,,405,59,63,80,65,80,58,1,False
9,Blastoise,Water,,530,79,83,100,85,105,78,1,False"
gen01 <- read.csv(textConnection=rawData,header=TRUE)
as.data.frame(names(gen01))
...and the output:
> as.data.frame(names(gen01))
names(gen01)
1 Number
2 Name
3 Type1
4 Type2
5 Total
6 HP
7 Attack
8 Defense
9 SpecialAtk
10 SpecialDef
11 Speed
12 Generation
13 Legendary
I recently reverted to R version 3.1.3 for compatibility reasons and am now encountering an unexplained error with the subset function.
I want to extract all rows for the gene "Migut.A00003" from the data frame transcr_effects using the gene name as listed in the data frame expr_mim_genes. (this will later become a loop). This action always returns all rows instead of specific rows I am looking for, no matter the formatting of the subset lookup:
> class(expr_mim_genes)
[1] "data.frame"
> sapply(expr_mim_genes, class)
gene longest.tr pair.length
"character" "logical" "numeric"
> head(expr_mim_genes)
gene longest.tr pair.length
1 Migut.A00003 NA 0
2 Migut.A00006 NA 0
3 Migut.A00007 NA 0
4 Migut.A00012 NA 0
5 Migut.A00014 NA 0
6 Migut.A00015 NA 0
> class(transcr_effects)
[1] "data.frame"
> sapply(transcr_effects, class)
pair gene
"character" "character"
> head(transcr_effects)
pair gene
1 pair1 Migut.N01020
2 pair10 Migut.A00351
3 pair1000 Migut.F00857
4 pair10007 Migut.D01637
5 pair10008 Migut.A00401
6 pair10009 Migut.G00442
. . .
7168 pair3430 Migut.A00003
. . .
The gene I am interested in:
> expr_mim_genes[1,"gene"]
[1] "Migut.A00003"
R sees these two terms as equivalent:
> expr_mim_genes[1,"gene"] == "Migut.A00003"
[1] TRUE
If I type in the name of the gene manually, the correct number of rows are returned:
> nrow(subset(transcr_effects, transcr_effects$gene=="Migut.A00003"))
[1] 1
> subset(transcr_effects, transcr_effects$gene=="Migut.A00003")
pair gene
7168 pair3430 Migut.A00003
However, this should return one row from the data.frame but it returns all rows:
> nrow(subset(transcr_effects, transcr_effects$gene == (expr_mim_genes[1,"gene"]))
[1] 10122
I have a feeling this has something to do with text formatting, but I've tried everything and haven't been able to figure it out. I've seen this issue with quoted v.s. unquoted entries, but it does not appear to be the issue here (see equality above).
I didn't have this problem before switching to R v.3.1.3, so maybe it is a version convention I am unaware of?
EDIT:
This is driving me crazy, but at least I think I have found a patch. There was quite a bit of data and file processing to get to this point in the code, involving loading at least 4 files. I've tried taking snippets of each file to post a reproducible example here, but sometimes when I analyze the snippets the error recurs, sometimes it does not (!!). After going through the process though, I discover that:
i = 1
gene = expr_mim_genes[i,"gene"]
> nrow(subset(transcr_effects, gene == gene))
[1] 10122
> nrow(subset(transcr_effects, gene == (expr_mim_genes[i,"gene"])))
[1] 1
I still can't explain this behavior of the code, but at least I know how to work around it.
Thanks all.