How can I make an list from existing data frame, each object in a list contains a vector of a single or multiple row from the data frame? - r

I am very new to R, still getting my head around so my question can be very basic but please help me out!
I have a large data frame, with more than 400000 rows.
GENE_ID p1 p2 p3 ...
41 1 2 3
41 4 5 6
41 7 8 9
85 1 2 3
1923 1 2 3
1923 4 5 6
First, I wanted to simply name the GENE_ID as the row name, but due to some gene IDs not unique, I failed.
Now I am thinking of making this data frame into a list each object contains expression level of a gene.
So what I want is a list that has outcome something like,
mylist$41
[1] 1 2 3 4 5 6 7 8 9
mylist$85
[1] 1 2 3
mylist$1923
[1] 1 2 3 4 5 6
Any advice to achieve this would be greatly appreciated.


We can do a melt by 'GENE_ID' and then do the split to get a list of vectors
library(reshape2)
mylist <- melt(df1, id.var = 'GENE_ID')
split(mylist$value, mylist$GENE_ID)
#$`41`
#[1] 1 4 7 2 5 8 3 6 9
#$`85`
#[1] 1 2 3
#$`1923`
#[1] 1 4 2 5 3 6
Also, we can do this in base R
v1 <- unlist(df1[-1], use.names = FALSE)
grp <- rep(df1[,1], ncol(df1[-1]))
split(v1, grp)

Related

Merge multiple data frames with partially matching rows

I have data frames with lists of elements such as NAMES. There are different names in dataframes, but most of them match together. I'd like to combine all of them in one list in which I'd see whether some names are missing from any of df.
DATA sample for df1:
X x
1 1 rh_Structure/Focus_S
2 2 rh_Structure/Focus_C
3 3 lh_Structure/Focus_S
4 4 lh_Structure/Focus_C
5 5 RH_Type-Function-S
6 6 RH_REFERENT-S
and for df2
X x
1 1 rh_Structure/Focus_S
2 2 rh_Structure/Focus_C
3 3 lh_Structure/Focus_S
4 4 lh_Structure/Focus_C
5 5 UCZESTNIK
6 6 COACH
and expected result would be:
NAME. df1 df2
1 COACH NA 6
2 lh_Structure/Focus_C 4 4
3 lh_Structure/Focus_S 3 3
4 RH_REFERENT-S 6 NA
5 rh_Structure/Focus_C 2 2
6 rh_Structure/Focus_S 1 1
7 RH_Type-Function-S 5 NA
8 UCZESTNIK NA 5
I can do that with merge.data.frame(df1,df2,by = "x", all=T),
but the I can't do it with more df with similar structure. Any help would be appreciated.

It might be easier to work with this in a long form. Just rbind all the datasets below one another with a flag for which dataset they came from. Then it's relatively straightforward to get a tabulation of all the missing values (and as an added bonus, you can see if you have any duplicates in any of the source datasets):
dfs <- c("df1","df2")
dfall <- do.call(rbind, Map(cbind, mget(dfs), src=dfs))
table(dfall$x, dfall$src)
# df1 df2
# COACH 0 1
# lh_Structure/Focus_C 1 1
# lh_Structure/Focus_S 1 1
# RH_REFERENT-S 1 0
# rh_Structure/Focus_C 1 1
# rh_Structure/Focus_S 1 1
# RH_Type-Function-S 1 0
# UCZESTNIK 0 1

How to check if rows in one column present in another column in R

I have a data set = data1 with id and emails as follows:
id emails
1 A,B,C,D,E
2 F,G,H,A,C,D
3 I,K,L,T
4 S,V,F,R,D,S,W,A
5 P,A,L,S
6 Q,W,E,R,F
7 S,D,F,E,Q
8 Z,A,D,E,F,R
9 X,C,F,G,H
10 A,V,D,S,C,E
I have another data set = data2 with check_email as follows:
check_email
A
D
S
V
I want to check if check_email column is present in data1 and want to take only those id from data1 when check_email in data2 is present in emails in data1.
My desired output will be:
id
1
2
4
5
7
8
10
I have created a code using for loop but it is taking forever because my actual dataset is very large.
Any advice in this regard will be highly appreciated!

You can use regular expression to subset your data. First collapse everything in one pattern:
paste(data2$check_email, collapse = "|")
# [1] "A|D|S|V"
Then create a indicator vector whether the pattern matches the emails:
grep(paste(data2$check_email, collapse = "|"), data1$emails)
# [1] 1 2 4 5 7 8 10
And then combine everything:
data1[grep(paste(data2$check_email, collapse = "|"), data1$emails), ]
# id emails
# 1 1 A,B,C,D,E
# 2 2 F,G,H,A,C,D
# 3 4 S,V,F,R,D,S,W,A
# 4 5 P,A,L,S
# 5 7 S,D,F,E,Q
# 6 8 Z,A,D,E,F,R
# 7 10 A,V,D,S,C,E

data1[rowSums(sapply(data2$check_email, function(x) grepl(x,data1$emails))) > 0, "id", F]
id
1 1
2 2
4 4
5 5
7 7
8 8
10 10

We can split the elements of the character vector as.character(data1$emails) into substrings, then we can iterate over this list with sapply looking for any value of this substring contained in data2$check_email. Finally we extract those values from data1
> emails <- strsplit(as.character(data1$emails), ",")
> ind <- sapply(emails, function(emails) any(emails %in% as.character(data2$check_email)))
> data1[ind,"id", drop = FALSE]
id
1 1
2 2
4 4
5 5
7 7
8 8
10 10

Order/Sort/Rank a table

I have a table like this
table(mtcars$gear, mtcars$cyl)
I want to rank the rows by the ones with more observations in the 4 cylinder. E.g.
4 6 8
4 8 4 0
5 2 1 2
3 1 2 12
I have been playing with order/sort/rank without much success. How could I order tables output?

We can convert table to data.frame and then order by the column.
sort_col <- "4"
tab <- as.data.frame.matrix(table(mtcars$gear, mtcars$cyl))
tab[order(-tab[sort_col]), ]
# OR tab[order(tab[sort_col], decreasing = TRUE), ]
# 4 6 8
#4 8 4 0
#5 2 1 2
#3 1 2 12
If we don't want to convert it into data frame and want to maintain the table structure we can do
tab <- table(mtcars$gear, mtcars$cyl)
tab[order(-tab[,dimnames(tab)[[2]] == sort_col]),]
# 4 6 8
# 4 8 4 0
# 5 2 1 2
# 3 1 2 12

Could try this. Use sort for the relevant column, specifying decreasing=TRUE; take the names of the sorted rows and subset using those.
table(mtcars$gear, mtcars$cyl)[names(sort(table(mtcars$gear, mtcars$cyl)[,1], dec=T)), ]
4 6 8
4 8 4 0
5 2 1 2
3 1 2 12

In the same scope as Milan, but using the order() function, instead of looking for names() in a sort()-ed list.
The [,1] is to look at the first column when ordering.
table(mtcars$gear, mtcars$cyl)[order(table(mtcars$gear, mtcars$cyl)[,1], decreasing=T),]

Build a data frame with overlapping observations

Lets say I have a data frame with the following structure:
> DF <- data.frame(x=1:5, y=6:10)
> DF
x y
1 1 6
2 2 7
3 3 8
4 4 9
5 5 10
I need to build a new data frame with overlapping observations from the first data frame to be used as an input for building the A matrix for the Rglpk optimization library. I would use n-length observation windows, so that if n=2 the resulting data frame would join rows 1&2, 2&3, 3&4, and so on. The length of the resulting data frame would be
(numberOfObservations-windowSize+1)*windowSize
The result for this example with windowSize=2 would be a structure like
x y
1 1 6
2 2 7
3 2 7
4 3 8
5 3 8
6 4 9
7 4 9
8 5 10
I could do a loop like
DFResult <- NULL
numBlocks <- nrow(DF)-windowSize+1
for (i in 1:numBlocks) {
DFResult <- rbind(DFResult, DF[i:(i+horizon-1), ])
}
But this seems vey inefficient, especially for very large data frames.
I also tried
rollapply(data=DF, width=windowSize, FUN=function(x) x, by.column=FALSE, by=1)
x y
[1,] 1 6
[2,] 2 7
[3,] 2 7
[4,] 3 8
where I was trying to repeat a block of rows without applying any aggregate function. This does not work since I am missing some rows
I am a bit stumped by this and have looked around for similar problems but could not find any. Does anyone have any better ideas?

We could do a vectorized approach
i1 <- seq_len(nrow(DF))
res <- DF[c(rbind(i1[-length(i1)], i1[-1])),]
row.names(res) <- NULL
res
# x y
#1 1 6
#2 2 7
#3 2 7
#4 3 8
#5 3 8
#6 4 9
#7 4 9
#8 5 10

create a vector from a given data frame row wise

in R I need to create a vector from a given data frame row wise. for example:
data frame:
A B
1 4
2 5
3 6
vector = 1 4 2 5 3 6
couldn't be so hard i think. Thanks so far.

> df <- data.frame(A=1:3,B=4:6)
> as.vector(t(df))
[1] 1 4 2 5 3 6

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