Assign multiple columns via vector without recycling - r

I am importing measurement data as a dataframe and want to include the experimental conditions in the data which are given in the filename. I want to add new columns to the dataframe that represent the conditions, and I want to assign the columns with the value specified by the filename. Later, this will facilitate comparisons to other experimental conditions once I merge the editted dataframes from each individual sample/file.
Here is an example of my pre-existing dataframe Measurements:
Measurements <- data.frame(
X = 1:4,
Length = c(130, 150, 170, 140)
)
Here are the example vectors of variables and values that would be derived from the filename:
FileVars.vec <- c("Condition", "Plant")
FileInfo.vec <- c("aKG", "1")
Here is one way that I have solved how to do what I want:
for (i in 1:length(FileVars.vec)) {
Measurements[FileVars.vec[i]] <- FileInfo.vec[i]
}
Which gives the desired output:
X Length Condition Plant
1 130 aKG 1
2 150 aKG 1
3 170 aKG 1
4 140 aKG 1
But my (limited) understanding of R is that it is a vectorized language that often avoids the need for using for-loops. I feel like this simpler code should work:
Measurements[FileVars.vec] <- FileInfo.vec
But instead of assigning one value for one entire column, it recycles the values within each column:
X Length Condition Plant
1 130 aKG aKG
2 150 1 1
3 170 aKG aKG
4 140 1 1
Is there any way to do a similar simple assignment but without recycling, i.e. one value is assigned to one full column only? I imagine there's a simple formatting fix but I've searched for a solution for >6 hours and no where did I see an assignment like this. I have also thought of creating a separate dataframe of just the experimental conditions and then merging to the actual dataframe, but that seems more roundabout to me, especially with more experimental conditions and observations than these examples.
Also, if there is a more established pipeline/package for taking information from the filename and adding it to the data in a tidy fashion, that would be marvelous as well! The original filename would be something like:
"aKG_1.csv"
Thank you for helping an R noobie! May you receive good coding karma when debugging!

We can convert to a list and then assign to avoid the recycling of values column wise. As it is a list, each element will be treated as a unit and the assignment occurs for the respectively columns by recycling those elements
Measurements[FileVars.vec] <- as.list(FileInfo.vec)
-output
Measurements
# X Length Condition Plant
#1 1 130 aKG 1
#2 2 150 aKG 1
#3 3 170 aKG 1
#4 4 140 aKG 1
If we want to reset the type, use type.convert
Measurements <- type.convert(Measurements, as.is = TRUE)
Note that by creating a vector for FileInfo.vec, it will have a single type i.e. character. Instead if we want to have multiple types, it can be a list
Measurements[FileVars.vec] <- list("akg", 1)
For the second part of the question, if we have a string
str1 <- "aKG_1.csv"
and wants to create two columns from that, either use, read.csv or strsplit
Measurements[FileVars.vec] <- read.table(text = tools::file_path_sans_ext(str1),
sep="_", header = FALSE)

Related

Removing extreme values in a dataframe while sorting for multiple columns R

I have a dataframe like this:
mydf <- data.frame(A = c(40,9,55,1,2), B = c(12,1345,112,45,789))
mydf
A B
1 40 12
2 9 1345
3 55 112
4 1 45
5 2 789
I want to retain only 95% of the observations and throw out 5% of the data that have extreme values. First, I calculate how many observations they are:
th <- length(mydf$A) * 0.95
And then I want to remove all the rows above the th (or retain the rows below the th, as you wish). I need to sort mydf in an ascending order, to remove only those extreme values. I tried several approaches:
mydf[order(mydf["A"], mydf["B"]),]
mydf[order(mydf$A,mydf$B),]
mydf[with(mydf, order(A,B)), ]
plyr::arrange(mydf,A,B)
but nothing works, so mydf is not sorted in ascending order by the two columns at the same time. I looked here Sort (order) data frame rows by multiple columns but the most common solutions do not work and I don't get why.
However, if I consider only one column at a time (e.g., A), those ordering methods work, but then I don't get how to throw out the extreme values, because this:
mydf <- mydf[(order(mydf$A) < th),]
removes the second row that has a value of 9, while my intent is to subset mydf retaining only the values below threshold (intended in this case as number of observations, not value).
I can imagine it is something very simple and basic that I am missing... And probably there are nicer tidyverse approaches.
I think you want rank here, but it doesn't work on multiple columns. To work around that, note that rank(.) is equivalent to order(order(.)):
rank(mydf$A)
# [1] 4 3 5 1 2
order(order(mydf$A))
# [1] 4 3 5 1 2
With that, we can order on both (all) columns, then order again, then compare the resulting ranks with your th value.
mydf[order(do.call(order, mydf)) < th,]
# A B
# 1 40 12
# 2 9 1345
# 4 1 45
# 5 2 789
This approach benefits from preserving the natural sort of the rows.
If you would prefer to stick with a single call to order, then you can reorder them and use head:
head(mydf[order(mydf$A, mydf$B),], th)
# A B
# 4 1 45
# 5 2 789
# 2 9 1345
# 1 40 12
though this does not preserve the original order of rows (which may or may not be important to you).
Possible approach
An alternative to your approach would be to use a dplyr ranking function such as cume_dist() or percent_rank(). These can accept a dataframe as input and return ranks / percentiles based on all columns.
set.seed(13)
dat_all <- data.frame(
A = sample(1:60, 100, replace = TRUE),
B = sample(1:1500, 100, replace = TRUE)
)
nrow(dat_all)
# 100
dat_95 <- dat_all[cume_dist(dat_all) <= .95, ]
nrow(dat_95)
# 95
General cautions about quantiles
More generally, keep in mind that defining quantiles is slippery, as there are multiple possible approaches. You'll want to think about what makes the most sense given your goal. As an example, from the dplyr docs:
cume_dist(x) counts the total number of values less than or equal to x_i, and divides it by the number of observations.
percent_rank(x) counts the total number of values less than x_i, and divides it by the number of observations minus 1.
Some implications of this are that the lowest value is always 1 / nrow() for cume_dist() but 0 for percent_rank(), while the highest value is always 1 for both methods. This means different cases might be excluded depending on the method. It also means the code I provided will always remove the highest-ranking row, which may or may not match your expectations. (e.g., in a vector with just 5 elements, is the highest value "above the 95th percentile"? It depends on how you define it.)

R: Dropping variables using number of observations

I have a large dataset, and I'm trying to drop some of my variables based on how many observations each has. For instance, I would like to drop any variable in my dataframe where n < 3 (total observations for that variable is less than 3). Since R can count observations for each variable using describe, can't I use that number to subset the data instead of having to type in each variable name each time I pull in a new version (each version has different variables that will have low n's and there are over 40 variables). Thanks so much for your help!
For instance, my data looks like this:
ID Runaway Aggressive Emergency Hospitalization Injury
1 3 NA 4 1 NA
2 NA NA 2 1 NA
3 4 NA 6 2 3
4 1 NA 1 1 NA
I want to be able to drop "Aggressive" and "Injury" based on their n's being 0 and 1 respectively. However, instead of telling R to drop them by variable name, it would be much more convenient if it was possible to tell R to drop any variable where n < 3 (or whatever number I choose) as I'll be using this code for multiple versions of this dataset. I have tried using column numbers (which is better than writing them out) but it's still pretty tedious when I have to describe() the data, figure out which variables have low n's, and then drop 28 variables or subset() around them.
This works but it's cumbersome...
UIRCorrelation <- UIRKidUnique61[c(28, 30, 32, 34:38, 42, 54:74)]
For some reason, my example looks different when I'm editing versus when I save so I also included an image of it. Sorry. This is the first time I've ever used stack overflow to ask a question. I actually spent a lot of time googling this but couldn't find an answer relating to n.
This line did not work: DF[, sapply(DF, function(col) length(na.omit(col))) > 4]
DF being your dataframe
DF[, sapply(DF, function(col) length(na.omit(col))) > 4]
This function did the trick:
valid <- function(x) {sum(!is.na(x))}
N <- apply(UIRCorrelation,2,valid)
UIRCorrelation2 <- UIRCorrelation[N > 3]

Get rows with common value into lists

I'm trying to get the rows according to the values in the "Type of region" column into lists and put these lists into a other data structure (vector or list).
The data looks like this (~700 000 lines):
chr CS CE CloneName score strand # locs per clone # capReg alignments Type of region
chr1 10027684 10028042 clone_11546 1 + 1 1 chr1_10027880_10028380_DNaseI
chr1 10027799 10028157 clone_11547 1 + 1 1 chr1_10027880_10028380_DNaseI
chr1 10027823 10028181 clone_11548 1 - 1 1 chr1_10027880_10028380_DNaseI
chr1 10027841 10028199 clone_11549 1 + 1 1 chr1_10027880_10028380_DNaseI
Here's what i tried to do:
typeReg=dat[!duplicated(dat$`Type of region`),]
for(i in 1:nrow(typeReg)){
res[[i]]=dat[dat$`Type of region`==typeReg[i,]$`Type of region`,]
}
The for loop took too much time so i tried using an apply:
res=apply(typeReg, 1, function(x){
tmp=dat[dat$`Type of region`==x[9],]
})
But it is also long (there are 300 000 unique values in the Type of region column).
Do you have a solution to my problem or is it normal that it's taking this long?
You can use split():
type <- as.factor(dat$Type_of_Region)
split(dat, type)
But, as stated in the comments, using dplyr::group_by() may be a better option depending on what you want to do later.
Ok, so split works but the subsetting doesn't drop levels of the factor i have in my df. So basically for every list the split function created, it brought the 300 000 levels in the original df thus the huge size of the list. The possible solutions are to use the droplevels() function on every list created (not optimal if one list is too big to store in the RAM), use a for loop (this solution is really slow) or to remove the columns that cause a problem which is what i did.
res=split(dat[,c(-4,-9)], dat$`Type of region`, drop=TRUE)

List all possible occurrences within a column?

I am trying to merge a data.frame and a column from another data.frame, but have so far been unsuccessful.
My first data.frame [Frequencies] consists of 2 columns, containing 47 upper/ lower case alpha characters and their frequency in a bigger data set. For example purposes:
Character<-c("A","a","B","b")
Frequency<-(100,230,500,420)
The second data.frame [Sequences] is 93,000 rows in length and contains 2 columns, with the 47 same upper/ lower case alpha characters and a corresponding qualitative description. For example:
Character<-c("a","a","b","A")
Descriptor<-c("Fast","Fast","Slow","Stop")
I wish to add the descriptor column to the [Frequencies] data.frame, but not the 93,000 rows! Rather, what each "Character" represents. For example:
Character<-c("a")
Frequency<-c("230")
Descriptor<-c("Fast")
Following can also be done:
> merge(adf, bdf[!duplicated(bdf$Character),])
Character Frequency Descriptor
1 a 230 Fast
2 A 100 Fast
3 b 420 Stop
4 B 500 Slow
Why not:
df1$Descriptor <- df2$Descriptor[ match(df1$Character, df2$Character) ]

Understanding the syntax for Column vs Row indexing in R

I'm a bit confused on the filtering scheme on an R data frame.
For example, let's say we have the following data frame titled dframe:
> str(dframe)
'data.frame': 143 obs. of 3 variables:
$ Year : int 1999 2005 2007 2008 2009 2010 2005 2006 2007 2008 ...
$ Name : Factor w/ 18 levels "AADAM","AADEN",..: 1 1 2 2 2 2 3 3 3 3 ...
$ Frequency: int 5 6 10 34 38 12 10 6 10 5 ...
Now if I want to filter dframe where the values of Name is of "AADAM", the proper filter is:
dframe[dframe$Name=="AADAM",]
The part where I'm confused is why the comma doesn't come first. Why isn't it this: dframe[,dframe$Name=="AARUSH"]
UPDATE: You clarified your question is really "Please give examples of what sort of logical expressions are valid for filtering columns?"
I agree with you the syntax appears weird initially, but it has the following logic.
The bottom line is that column-filter expressions are typically less rich and expressive than row-filtering expressions, and in particular you can't chain logical indexing the way you do with rows.
Best way is to think of indexing expressions as the general form:
dframe[<row-index-expression>,<col-index-expression>]
where either index-expression is optional, so you can just do one and we (crucially!) need the comma to disambiguate whether it's row- or column-indexing:
dframe[<row-index-expression>,] # such as dframe[dframe$Name=="ADAM",]
dframe[,<col-index-expression>]
Before we look at examples of col-index-expression and what's valid (and invalid) to include in one, let's review and discuss how R does indexing - I had the same confusion when I started with it.
In this example, you have three columns. You can refer to them by their string names 'Year','Name','Frequency'. You can also refer to them by column indices 1,2,3 where the numbers 1,2,3 correspond to the entries colnames(dframe). R does indexing using the '[' operator, also the '[[' operator. Here are some valid examples of ways to index column-indexing:
dframe[,2] # column 2 / Name
dframe[,'Name'] # column 2 / Name
dframe[,c('Name','Frequency')] # string vector - very common
dframe[,c(2,3)] # integer vector - also very common
dframe[,c(F,T,T)] # logical vector - very rarely seen, and a pain in the butt to compute
Now, if you choose to use a logical expression for the column-index, it must be a valid expression without using column names - inside a column it doesn't know their own names.
Suppose you wanted to dynamically filter "give me only the factor columns from dframe".
Something like:
unlist(apply(dframe[1,1:3], 2, is.factor), use.names=F) # except I can't seem to remove the colnames
For more help and examples on indexing look at the '[' operator help-page:
Type ?'['
dframe[,dframe$Name=="ADAM"] is invalid attempt at column-indexing because the columns know nothing about Name=="ADAM"
Addendum: code to generate example dataframe (because you didn't dump us a dput output)
set.seed(123)
N = 10
randomName <- function() { cat(sample(letters, size=runif(1)*6+2, replace=T), sep='') }
dframe = data.frame(Year=round(runif(N,1980,2014)),
Name = as.factor(replicate(N, randomName())),
Frequency=round(runif(N, 2,40)))
You have to remember that when you're sub-setting, the part before the comma is specifying which rows you want, and the part after the comma is specifying which columns you want. ie:
dframe[rowsyouwant, columnsyouwant]
You're filtering based on columns, but you want all of the columns in your result, so the space after the comma is blank. You want some sub-set of rows, so your filtering specification goes before the comma, where the rows you want are specified.
As others have indicated, requesting a certain subset of a data frame requires the syntax [rows, columns]. Since dframe[has 143 rows, has 3 columns], any request for some part of dframe should be of the form
dframe[which of the 143 rows do I want?, which of the 3 columns do I want?].
Because dframe$Name is a vector of length 143, the comparison dframe$Name=='AADAM' is a vector of T/F values that also has length 143. So,
dframe[dframe$Name=='AADAM',]
is like saying
dframe[of the 143 rows I want these ones, I want all columns]
whereas
dframe[,dframe$Name=='AADAM']
generates an error because it's like saying
dframe[I want all rows, of the 143 columns I want these ones]
On a side note, you may want to look into the subset() function if you're not already familiar with it. You could get the same result by writing subset(dframe, Name=='AADAM')
As others have said, the structure within brackets is row, then column.
One way I think of the syntax of selecting data from a data.frame using:
dframe[dframe$Name=="AADAM",]
is to think of a noun, then a verb where:
dframe[] is the noun. It is the object on which you want to perform an action
and
[dframe$Name=="AADAM",] is the verb. It is the action you want to perform.
I have a silly way of expressing this to myself, but it keeps things straight in my mind:
Hey, you! dframe! I am going to... ...in this case, select all of your rows in which Name is equal to AADAM!
By keeping the column portion of [dframe$Name=="AADAM",] blank you are saying you want to keep all columns.
Sometimes it can be a little difficult to remember that you have to write dframe both inside and outside the brackets.
As for exactly why row comes first and column comes second, I do not know, but row had to be either first or second.
dframe <- read.table(text = '
Year Name Frequency
1 ADAM 4
3 BOB 10
7 SALLY 5
2 ADAM 12
4 JIM 3
12 ADAM 7
', header = TRUE)
dframe[,dframe$Name=="ADAM"]
# Error in `[.data.frame`(dframe, , dframe$Name == "ADAM") :
# undefined columns selected
dframe[dframe$Name=="ADAM",]
# Year Name Frequency
# 1 1 ADAM 4
# 4 2 ADAM 12
# 6 12 ADAM 7
dframe[,'Name']
# [1] ADAM BOB SALLY ADAM JIM ADAM
# Levels: ADAM BOB JIM SALLY
dframe[dframe$Name=="ADAM",'Name']
# [1] ADAM ADAM ADAM
# Levels: ADAM BOB JIM SALLY

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