I have dataframe like this:
Hashed_User_Id
[1] f2de2b4a6011a1ab52d3aefbc9b8a4103d7574f4
[2] 88cb5d85c41abb7ad99595ceb7c2fc98409dd4dc
[3] 25313021517412ce58072d798ccea29ba5d2f427
[4] f2de2b4a6011a1ab52d3aefbc9b8a4103d7574f4
[5] 88cb5d85c41abb7ad99595ceb7c2fc98409dd4dc
[6] 25313021517412ce58072d798ccea29ba5d2f427
I want to replace these hashed values by numeric values keeping same number for same values, something like this:
Hashed_User_Id
[1] 1
[2] 2
[3] 3
[4] 1
[5] 2
[6] 3
How can I achieve this?
As Ronak suggested,
as.integer(as.factor(Hashed_User_Id))
Related
I want to remove the dashes and keep only the first 4 substrings except for the last character.
sub.maf.barcode <- gsub("^([^-]*-[^-]*-[^-]*-[^-]*).{1}$", "\\1", ori.maf.barcode$Tumor_Sample_Barcode)
> ori.maf.barcode$Tumor_Sample_Barcode[1:5]
[1] "TCGA-2K-A9WE-01A-11D-A382-10" "TCGA-2Z-A9J1-01A-11D-A382-10"
[3] "TCGA-2Z-A9J2-01A-11D-A382-10" "TCGA-2Z-A9J3-01A-12D-A382-10"
[5] "TCGA-2Z-A9J5-01A-21D-A382-10"
Expected output:
[1] "TCGA-2K-A9WE-01" "TCGA-2Z-A9J1-01"
[3] "TCGA-2Z-A9J2-01" "TCGA-2Z-A9J3-01"
[5] "TCGA-2Z-A9J5-01"
You could do
gsub('.-[^-]*-[^-]*-.[^-]*$', "", ori.maf.barcode$Tumor_Sample_Barcode)
#> [1] "TCGA-2K-A9WE-01" "TCGA-2Z-A9J1-01" "TCGA-2Z-A9J2-01"
#> [4] "TCGA-2Z-A9J3-01" "TCGA-2Z-A9J5-01"
Or
substr(ori.maf.barcode$Tumor_Sample_Barcode, 1, 15)
#> [1] "TCGA-2K-A9WE-01" "TCGA-2Z-A9J1-01" "TCGA-2Z-A9J2-01"
#> [4] "TCGA-2Z-A9J3-01" "TCGA-2Z-A9J5-01"
using str_extract
library(stringr)
str_extract(ori.maf.barcode$Tumor_Sample_Barcode, "^([^-]+-){3}\\d+")
-output
[1] "TCGA-2K-A9WE-01" "TCGA-2Z-A9J1-01" "TCGA-2Z-A9J2-01"
[4] "TCGA-2Z-A9J3-01" "TCGA-2Z-A9J5-01"
How would I go about extracting, for each row (there are ~56,000 records in an Excel file) in a specific column, only part of a string? I need to keep all text to the left of the last '/' forward slash. The challenge is that not all cells have the same number of '/'. There is always a filename (*.wav) at the end of the last '/', but the number of characters in the filename is not always the same (sometimes 5 and sometimes 6).
Below are some examples of the strings in the cells:
cloch/51.wav
grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav
grand/Grand_bombarde/02-suchy_Grand_bombarde/039-D#.wav
AB_AeolinaL/025-C#.wav
AB_AeolinaL/026-D.wav
AB_violadamourL/rel99999/091-G.wav
AB_violadamourL/rel99999/092-G#.wav
AB_violadamourR/024-C.wav
AB_violadamourR/025-C#.wav
The extracted text should be:
cloch
grand/Grand_bombarde/02-suchy_Grand_bombarde
grand/Grand_bombarde/02-suchy_Grand_bombarde
AB_AeolinaL
AB_AeolinaL
AB_violadamourL/rel99999
AB_violadamourL/rel99999
AB_violadamourR
AB_violadamourR
Can anyone recommend a strategy using R?
You can use the stringr package str_remove(string,pattern) function like:
str = "grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav"
str_remove(str,"/[0-9]+[-]*[A-Z]*[#]*[.][a-z]+")
Output:
> str_remove(str,"/[0-9]+[-]*[A-Z]*[#]*[.][a-z]+")
[1] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
Then you can just iterate over all other strings:
strings <- c("cloch/51.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/039-D#.wav",
"AB_AeolinaL/025-C#.wav",
"AB_AeolinaL/026-D.wav",
"AB_violadamourL/rel99999/091-G.wav",
"AB_violadamourL/rel99999/092-G#.wav",
"AB_violadamourR/024-C.wav",
"AB_violadamourR/025-C#.wav")
str_remove(strings,"/[0-9]+[-]*[A-Z]*[#]*[.][a-z]+")
Output:
> str_remove(strings,"/[0-9]+[-]*[A-Z]*[#]*[.][a-z]+")
[1] "cloch"
[2] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[3] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[4] "AB_AeolinaL"
[5] "AB_AeolinaL"
[6] "AB_violadamourL/rel99999"
[7] "AB_violadamourL/rel99999"
[8] "AB_violadamourR"
[9] "AB_violadamourR"
You have to substract strings using this method:
substr(strings,1,regexpr("\\/[^\\/]*$", strings)-1)
[1] "cloch"
[2] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[3] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[4] "AB_AeolinaL"
[5] "AB_AeolinaL"
[6] "AB_violadamourL/rel99999"
[7] "AB_violadamourL/rel99999"
[8] "AB_violadamourR"
[9] "AB_violadamourR"
Input
strings<-c("cloch/51.wav","grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav","grand/Grand_bombarde/02-suchy_Grand_bombarde/039-D#.wav","AB_AeolinaL/025-C#.wav","AB_AeolinaL/026-D.wav","AB_violadamourL/rel99999/091-G.wav","AB_violadamourL/rel99999/092-G#.wav","AB_violadamourR/024-C.wav","AB_violadamourR/025-C#.wav")
In which this regex regexpr("\\/[^\\/]*$", strings) gives you the position of the last "/"
Assuming that the strings you propose are in a column of a dataframe:
df <- data.frame(x = 1:5, y = c("cloch/51.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/039-D#.wav",
"AB_AeolinaL/025-C#.wav",
"AB_AeolinaL/026-D.wav"))
# I define a function that separates a string at each "/"
# throws the last piece and reattaches the pieces
cut_str <- function(s) {
st <- head((unlist(strsplit(s, "\\/"))), -1)
r <- paste(st, collapse = "/")
return(r)
}
# through the sapply function I get the desired result
new_strings <- as.vector(sapply(df$y, FUN = cut_str))
new_strings
[1] "cloch"
[2] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[3] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[4] "AB_AeolinaL"
[5] "AB_AeolinaL"
You could use
dirname(strings)
If there is no /, this returns ., which you could remove afterwards if you like, e.g.:
res <- dirname(strings)
res[res=="."] <- ""
``
You could start the match with / followed by 1 or more times any char except a forward slash or a whitespace char using a negated character class [^\\s/]+
Then match .wav at the end of the string using $
Replace the match with an empty string using sub for example.
[^\\s/]+\\.wav$
See the regex matches | R demo
strings <- c("cloch/51.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/038-D.wav",
"grand/Grand_bombarde/02-suchy_Grand_bombarde/039-D#.wav",
"AB_AeolinaL/025-C#.wav",
"AB_AeolinaL/026-D.wav",
"AB_violadamourL/rel99999/091-G.wav",
"AB_violadamourL/rel99999/092-G#.wav",
"AB_violadamourR/024-C.wav",
"AB_violadamourR/025-C#.wav")
sub("/[^\\s/]+\\.wav$", "", strings)
Output
[1] "cloch"
[2] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[3] "grand/Grand_bombarde/02-suchy_Grand_bombarde"
[4] "AB_AeolinaL"
[5] "AB_AeolinaL"
[6] "AB_violadamourL/rel99999"
[7] "AB_violadamourL/rel99999"
[8] "AB_violadamourR"
[9] "AB_violadamourR"
I have a data frame in R with 341 rows. I want to rename the row names using a list with 349 names. All 341 names will be in this list for sure. But not all of them will be perfect hits.
The data looks like this
rownames(df_RPM1)
[1] "LQNS02059392.1_11686_5p"
[2] "LQNS02277998.1_30984_3p"
[3] "LQNS02277998.1_30984_5p"
[4] "LQNS02277998.1_30988_3p"
[5] "LQNS02277998.1_30988_5p"
[6] "LQNS02277997.1_30943_3p"
[7] "miR-9|LQNS02278070.1_31740_3p"
[8] "miR-9|LQNS02278094.1_36129_3p"
head(inlist)
[1] "dpu-miR-2-03_LQNS02059392.1_11686_5p" "dpu-miR-10-P2_LQNS02277998.1_30984_3p"
[3] "dpu-miR-10-P2_LQNS02277998.1_30984_5p" "dpu-miR-10-P3_LQNS02277998.1_30988_3p"
[5] "dpu-miR-10-P3_LQNS02277998.1_30988_5p" "miR-9|LQNS02278070.1_31740_3p"
[6] "miR-9|LQNS02278094.1_36129_3p"
The order won't necessarily be the same in the two.
Can anyone suggest me how to do this in R?
Thanks a lot
Depends a lot what a "non-perfect hit" looks like. Assuming the row name is a substring of the real name, str_detect() does the job quite well:
library(tidyverse)
real_names <- c("dpu-miR-2-03_LQNS02059392.1_11686_5p",
"dpu-miR-10-P2_LQNS02277998.1_30984_3p",
"dpu-miR-10-P2_LQNS02277998.1_30984_5p",
"dpu-miR-10-P3_LQNS02277998.1_30988_3p",
"dpu-miR-10-P3_LQNS02277998.1_30988_5p",
"miR-9|LQNS02278070.1_31740_3p",
"miR-9|LQNS02278094.1_36129_3p")
str_which(real_names, "LQNS02059392.1_11686_5p")
#> [1] 1
So we can vectorize (I removed the element 6 which is not found in the example list):
pos <- map_int(rownames(df_RPM1), ~ str_which(real_names, fixed(.)))
pos
#> [1] 1 2 3 4 5 6 7
And all that's left is to change the row names:
rownames(df_RPM1) <- real_names[pos]
Of course, if a non-perfect hit means something more complicated, you may need to create a regex from the row names or something like that.
I have a csv file like this,
x <- read.csv("C:/Users/XXXX/Documents/XXXX/Day1_15042014/work2.csv")
class(x)
x$Sequence.window![enter image description here][1]
> x$Sequence.window
[1] VVELRKTGGDTLEFHKFYKNFSSGLKDVVWN
[2] PGLTTQGTKFGRKIVKTLAYRVKSTQPSSGN
[3] EATEFYLRYYVGHKGKFGHEFLEFEFREDGK
[4] LVPVVWGERKTPEIEKKGFGASSKAATSLPS
[5] NMNELPEKKNSAGFIKLEDKQKLIVEMEKSV
[6] PTLHFNYRYFETDAPKDVPGAPRQWWFGGGT
[7] PDPTTAPMEAAKQPKKKRSRSKKCKSVNNLD
[8] PAKAAKTAKVTSPAKKAVAATKKVATVATKK
The class of this is a dataframe . I would now like to split the sequence window within a range 10:22 ( Ex [1] VVELRKTGGDTLEFHKFYKNFSSGLKDVVWN, output should be like [1] DTLEFHKFYKNFS for all the sequences) . How would I do this within a data frame?
You can use the substr function
#dummy data
x <- read.table(text="Sequence.window
VVELRKTGGDTLEFHKFYKNFSSGLKDVVWN
PGLTTQGTKFGRKIVKTLAYRVKSTQPSSGN
EATEFYLRYYVGHKGKFGHEFLEFEFREDGK",header=TRUE,as.is=TRUE)
#substr from 10 to 22
substr(x$Sequence.window,start=10,stop=22)
#[1] "DTLEFHKFYKNFS" "FGRKIVKTLAYRV" "YVGHKGKFGHEFL"
I have a vector of strings that contain both character and numeric values. For example:
a=c("ILLUMINA:420:C2D7UACXX:1:1102:14591:91480","ILLUMINA:420:C2D7UACXX:1:1102:14592:3881","ILLUMINA:420:C2D7UACXX:1:1102:14592:37103","ILLUMINA:420:C2D7UACXX:1:1102:14592:37356")
I'd like to order the vector so that the characters are sorted alphabetically and the numbers numerically. The structure of the strings is always of the format:
"ILLUMINA:420:C2D7UACXX:1:<number>:<number>:<number>", so actually the order only applies to the last three colon separated numbers.
I did try mixedsort {gtools} but the result was the same as using sort and
sort.int, which is:
> mixedsort(a)
[1] "ILLUMINA:420:C2D7UACXX:1:1102:14591:91480" "ILLUMINA:420:C2D7UACXX:1:1102:14592:37103"
[3] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37356" "ILLUMINA:420:C2D7UACXX:1:1102:14592:3881"
Clearly the right order should be:
[1] "ILLUMINA:420:C2D7UACXX:1:1102:14591:91480" "ILLUMINA:420:C2D7UACXX:1:1102:14592:3881"
[3] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37103" "ILLUMINA:420:C2D7UACXX:1:1102:14592:37356"
Is there any immediate solution?
EDIT completely change the solution after OP clarification
You can extract the last 3 elements and order, and you create a data.frame:
dat = read.table(text=sub('.*:1:([0-9]+):([0-9]+):([0-9]+)','\\1|\\2|\\3',a),sep='|')
dat
V1 V2 V3
1 1102 14591 91480
2 1102 14592 3881
3 1102 14592 37103
4 1102 14592 37356
Then you order using 3 columns:
a[with(dat,order(V1,V2,V3))]
[1] "ILLUMINA:420:C2D7UACXX:1:1102:14591:91480" "ILLUMINA:420:C2D7UACXX:1:1102:14592:3881"
[3] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37103" "ILLUMINA:420:C2D7UACXX:1:1102:14592:37356"
gtools::mixedsort does work in your case, actually:
> a=c("ILLUMINA:420:C2D7UACXX:1:1102:14591:91480",
"ILLUMINA:420:C2D7UACXX:1:1102:14592:3881",
"ILLUMINA:420:C2D7UACXX:1:1102:14592:37103",
"ILLUMINA:420:C2D7UACXX:1:1102:14592:37356")
>
> mixedsort(a)
[1] "ILLUMINA:420:C2D7UACXX:1:1102:14591:91480"
[2] "ILLUMINA:420:C2D7UACXX:1:1102:14592:3881"
[3] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37103"
[4] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37356"
I am using gtools_3.4.2 and R-3.2.0
Here's a faster solution:
fields.list = strsplit(a,split=":")
sort.dt = data.table(t(sapply(fields.list,function(x) as.numeric(c(x[5],x[6],x[7])))))
sorted.a = v[with(sort.dt,order(V1,V2,V3))]
> sorted.a
[1] "ILLUMINA:420:C2D7UACXX:1:1102:14591:91480" "ILLUMINA:420:C2D7UACXX:1:1102:14592:3881" "ILLUMINA:420:C2D7UACXX:1:1102:14592:37103"
[4] "ILLUMINA:420:C2D7UACXX:1:1102:14592:37356"