Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.
On Sat, 18 Oct 2014, Anna Zakrisson Braeunlich wrote:
Thank you! That was a easy and fast solution!
If it was so easy, why couldn't you adapt Ista's solution? I suspect
it is because you don't understand his suggestion.
May I post a follow-up question? (I am not sure if this would rather
should be posted as a new question, but I post it here and then I can
re-post it if this is the wrong place to ask this). I am ever so
grateful for your help!
This probably should have been a new thread, but I will bite anyway.
/Anna
# FOLLOW-UP QUESTION
df1 - data.frame(cbind(Identifier = c(M123.B23.VJHJ, M123.B24.VJHJ,
M123.B23.VLKE, M123.B23.HKJH,
M123.B24.LKJH),
Sequence = c(ATATATATATA, ATATATATATA,
ATATAGCATATA,
ATATATAGGGTA,
ATCGCGCGAATA)))
Just because R has a habit of making factors at the drop of a hat doesn't
mean that if your data are still not ready to be treated as factors that
you have to accept what it does. When you read the data in via read.csv
you can use the colClasses argument or the stringsAsFactors argument to
stop that. You can use stringsAsFactors when you create the data frame
also, and you can always go back and turn any particular column into a
factor after you are done manipulating characters.
Also, somewhere you picked up the bad habit of using cbind before you make
your data frame... that is almost never a good idea, because in data
frames each column can be have its own storage mode, while cbind creates a
matrix where every element must have the same storage mode.
df1 - data.frame( Identifier = c( M123.B23.VJHJ, M123.B24.VJHJ
, M123.B23.VLKE, M123.B23.HKJH
, M123.B24.LKJH )
, Sequence = c( ATATATATATA, ATATATATATA
, ATATAGCATATA, ATATATAGGGTA
, ATCGCGCGAATA )
, stringsAsFactors=FALSE
)
# as a follow-up question:
# How can I split the identifier in df1 above into several columns based on the
# separating dots? The real data includes thousands of rows.
# This is what I want it to look like in the end:
df1_solution - data.frame(cbind(Identifier1 = c(M123, M123,
M123, M123,
M123),
Identifier2 = c(B23, B24, B23, B23, B24),
Identifier3 = c(VJHJ, VJHJ, VLKE, HKJH, LKJH),
Sequence = c(ATATATATATA, ATATATATATA,
ATATAGCATATA, ATATATAGGGTA,
ATCGCGCGAATA)))
df1_solution - data.frame( Identifier1 = c( M123, M123
, M123, M123
, M123 )
, Identifier2 = c( B23, B24, B23
, B23, B24 )
, Identifier3 = c( VJHJ, VJHJ
, VLKE, HKJH, LKJH)
, Sequence = c( ATATATATATA, ATATATATATA
, ATATAGCATATA, ATATATAGGGTA
, ATCGCGCGAATA )
, stringsAsFactors=FALSE
)
# I am very grateful for your help! I am no whiz at R and everything I know
# is self-taught. Therefore, some basics can turn out to be quite some
# obsatcles for me.
# /Anna
Pretty much all of us are here to teach ourselves R, Anna. Keep reading
other people's questions. Learn to try each fragment alone at the command
line to figure out what is happening. Use the str() function frequently.
# the basic split
parts - strsplit( as.character( df1$Identifier ), ., fixed=TRUE )
# extension of Ista's approach to assembly
ans1 - data.frame( Identifier1 = rep( NA, nrow( ans1 ) )
, Identifier2 = rep( NA, nrow( ans1 ) )
, Identifier3 = rep( NA, nrow( ans1 ) )
, stringsAsFactors = FALSE
)
# note all memory is pre-allocated above... avoid successively
# accumulating rows with rbind... that would be very slow
for ( rw in seq_along( df1$Identifier ) ) {
v - parts[[ rw ]]
ans1[ rw, Identifier1 ] - v[ 1 ]
ans1[ rw, Identifier2 ] - v[ 2 ]
ans1[ rw, Identifier3 ] - v[ 3 ]
}
ans1$Sequence - df1$Sequence
# alternative method of assembly
# uses list-to-data.frame apply from plyr package
library(plyr)
ans2 - ldply( parts
, function( v ) { # called once for each item in parts list
# all single-row data frames created in this
# function are concatenated at once by ldply to
Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.
Hi Jeff an many thank's for your time. I meant that it was easy as in not requiring som many steps... I have managed to get it to run and it has solved my problem perfectly. Thank you for all your tips and instructions! Up until now, I have used excel for all problems similar to this one and only used R for the statistics part. I intend to make a permanent swith to R as I can see the benefits. I am just severely frustrated by my own inabilities. Therefore, once again many thank´s for your time! kind regards Anna º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•. .• `•. .º Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin Germany/Deutschland E-mail: anna.zakris...@su.se Tel work: +49-(0)3091541281 Mobile: +49-(0)15777374888 LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•. .• `•. .º From: Jeff Newmiller [jdnew...@dcn.davis.ca.us] Sent: 19 October 2014 08:25 To: Anna Zakrisson Braeunlich Cc: Ista Zahn; r-help@r-project.org Subject: Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data. On Sat, 18 Oct 2014, Anna Zakrisson Braeunlich wrote: Thank you! That was a easy and fast solution! If it was so easy, why couldn't you adapt Ista's solution? I suspect it is because you don't understand his suggestion. May I post a follow-up question? (I am not sure if this would rather should be posted as a new question, but I post it here and then I can re-post it if this is the wrong place to ask this). I am ever so grateful for your help! This probably should have been a new thread, but I will bite anyway. /Anna # FOLLOW-UP QUESTION df1 - data.frame(cbind(Identifier = c(M123.B23.VJHJ, M123.B24.VJHJ, M123.B23.VLKE, M123.B23.HKJH, M123.B24.LKJH), Sequence = c(ATATATATATA, ATATATATATA, ATATAGCATATA, ATATATAGGGTA, ATCGCGCGAATA))) Just because R has a habit of making factors at the drop of a hat doesn't mean that if your data are still not ready to be treated as factors that you have to accept what it does. When you read the data in via read.csv you can use the colClasses argument or the stringsAsFactors argument to stop that. You can use stringsAsFactors when you create the data frame also, and you can always go back and turn any particular column into a factor after you are done manipulating characters. Also, somewhere you picked up the bad habit of using cbind before you make your data frame... that is almost never a good idea, because in data frames each column can be have its own storage mode, while cbind creates a matrix where every element must have the same storage mode. df1 - data.frame( Identifier = c( M123.B23.VJHJ, M123.B24.VJHJ , M123.B23.VLKE, M123.B23.HKJH , M123.B24.LKJH ) , Sequence = c( ATATATATATA, ATATATATATA , ATATAGCATATA, ATATATAGGGTA , ATCGCGCGAATA ) , stringsAsFactors=FALSE ) # as a follow-up question: # How can I split the identifier in df1 above into several columns based on the # separating dots? The real data includes thousands of rows. # This is what I want it to look like in the end: df1_solution - data.frame(cbind(Identifier1 = c(M123, M123, M123, M123, M123), Identifier2 = c(B23, B24, B23, B23, B24), Identifier3 = c(VJHJ, VJHJ, VLKE, HKJH, LKJH), Sequence = c(ATATATATATA, ATATATATATA, ATATAGCATATA, ATATATAGGGTA, ATCGCGCGAATA))) df1_solution - data.frame( Identifier1 = c( M123, M123 , M123, M123 , M123 ) , Identifier2 = c( B23, B24, B23 , B23, B24 ) , Identifier3 = c( VJHJ, VJHJ , VLKE, HKJH, LKJH) , Sequence = c( ATATATATATA, ATATATATATA , ATATAGCATATA, ATATATAGGGTA , ATCGCGCGAATA ) , stringsAsFactors=FALSE
Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.
Thank you! That was a easy and fast solution!
May I post a follow-up question? (I am not sure if this would rather should be
posted as a new question, but I post it here and then I can re-post it if this
is the wrong place to ask this). I am ever so grateful for your help!
/Anna
# FOLLOW-UP QUESTION
df1 - data.frame(cbind(Identifier = c(M123.B23.VJHJ, M123.B24.VJHJ,
M123.B23.VLKE, M123.B23.HKJH,
M123.B24.LKJH),
Sequence = c(ATATATATATA,
ATATATATATA,
ATATAGCATATA,
ATATATAGGGTA,
ATCGCGCGAATA)))
# as a follow-up question:
# How can I split the identifier in df1 above into several columns based on the
# separating dots? The real data includes thousands of rows.
# This is what I want it to look like in the end:
df1_solution - data.frame(cbind(Identifier1 = c(M123, M123,
M123, M123,
M123),
Identifier2 = c(B23, B24, B23, B23, B24),
Identifier3 = c(VJHJ, VJHJ, VLKE, HKJH, LKJH),
Sequence = c(ATATATATATA, ATATATATATA,
ATATAGCATATA, ATATATAGGGTA,
ATCGCGCGAATA)))
# I am very grateful for your help! I am no whiz at R and everything I know
# is self-taught. Therefore, some basics can turn out to be quite some
# obsatcles for me.
# /Anna
º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•. .•
`•. .º
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•. .•
`•. .º
From: Ista Zahn [istaz...@gmail.com]
Sent: 13 October 2014 15:42
To: Anna Zakrisson Braeunlich
Cc: r-help@r-project.org
Subject: Re: [R] seqinr ?: Splitting a factor name into several columns.
Dealing with metabarcoding data.
Hi Anna,
On Sun, Oct 12, 2014 at 3:24 AM, Anna Zakrisson Braeunlich
anna.zakris...@su.se wrote:
Hi,
I have a question how to split a factor name into different columns. I have
metabarcoding data and need to merge the FASTA-file with the taxonomy- and
counttable files (dataframes). To be able to do this merge, I need to isolate
the common identifier, that unfortunately is baked in with a lot of other
labels in the factor name eg:
sequence identifier:
M01271_77_0.A8J0P_1_1101_10150_1525.1.322519.sample_1.sample_2
I want to split this name at every . to get several columns:
column1: M01271_77_0
column2: A8J0P_1_1101_10150_1525
column3: 1
column4: 322519
column5: sample_1
column6: sample_2
I must add that I have no influence on how these names are given. This is how
thay are supplied from Illumina Miseq. I just need to be able to deal with it.
Here is some extremely simplified dummy data to further show the issue at
hand:
df1 - data.frame(cbind(X = 1:10, Y = rnorm(10)),
Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each =
5)))
df2 - data.frame(cbind(B = 13:22, K = rnorm(10)),
Q.identifierA.B4668726 = factor(rep(LETTERS[1:2], each =
5)))
# I have metabarcoding data with one FASTA-file, one count table and one
taxonomy file
# Above dummy data is just showing the issue at hand. I want to be able to
merge my three
# original data frames (here, the dummy data is only two dataframes). The
problem is that
# the only identifier that is commmon for the dataframes is hidden in the
# factor name eg: Z.identifierA.1298712 and Q.identifierA.4668726. I hence
need to be able
# to split this name up into different columns to get identifierA alone as
one column name
# Then I can merge the dataframes.
# How can I do this in R. I know that it can be done in excel, but I would
like to
# produce a complete R-script to get a fast pipeline and avoid copy and paste
errors.
# This is what I want it to look:
df1.goal - data.frame(cbind(X = 1:10, Y = rnorm(10)),
Z = factor(rep(LETTERS[1:2], each = 5)),
identifierA = factor(rep(LETTERS[1:2], each = 5)),
B1298712 = factor(rep(LETTERS[1:2], each = 5)))
Use strsplit to separate the components, something like
separateNames - strsplit(names(df1)[3], split = \\.)[[1]]
for(name in separateNames) {
df1[[name]] - df1[[3]]
}
df1[[3]] - NULL
Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.
Hi Anna,
On Sun, Oct 12, 2014 at 3:24 AM, Anna Zakrisson Braeunlich
anna.zakris...@su.se wrote:
Hi,
I have a question how to split a factor name into different columns. I have
metabarcoding data and need to merge the FASTA-file with the taxonomy- and
counttable files (dataframes). To be able to do this merge, I need to isolate
the common identifier, that unfortunately is baked in with a lot of other
labels in the factor name eg:
sequence identifier:
M01271_77_0.A8J0P_1_1101_10150_1525.1.322519.sample_1.sample_2
I want to split this name at every . to get several columns:
column1: M01271_77_0
column2: A8J0P_1_1101_10150_1525
column3: 1
column4: 322519
column5: sample_1
column6: sample_2
I must add that I have no influence on how these names are given. This is how
thay are supplied from Illumina Miseq. I just need to be able to deal with it.
Here is some extremely simplified dummy data to further show the issue at
hand:
df1 - data.frame(cbind(X = 1:10, Y = rnorm(10)),
Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each =
5)))
df2 - data.frame(cbind(B = 13:22, K = rnorm(10)),
Q.identifierA.B4668726 = factor(rep(LETTERS[1:2], each =
5)))
# I have metabarcoding data with one FASTA-file, one count table and one
taxonomy file
# Above dummy data is just showing the issue at hand. I want to be able to
merge my three
# original data frames (here, the dummy data is only two dataframes). The
problem is that
# the only identifier that is commmon for the dataframes is hidden in the
# factor name eg: Z.identifierA.1298712 and Q.identifierA.4668726. I hence
need to be able
# to split this name up into different columns to get identifierA alone as
one column name
# Then I can merge the dataframes.
# How can I do this in R. I know that it can be done in excel, but I would
like to
# produce a complete R-script to get a fast pipeline and avoid copy and paste
errors.
# This is what I want it to look:
df1.goal - data.frame(cbind(X = 1:10, Y = rnorm(10)),
Z = factor(rep(LETTERS[1:2], each = 5)),
identifierA = factor(rep(LETTERS[1:2], each = 5)),
B1298712 = factor(rep(LETTERS[1:2], each = 5)))
Use strsplit to separate the components, something like
separateNames - strsplit(names(df1)[3], split = \\.)[[1]]
for(name in separateNames) {
df1[[name]] - df1[[3]]
}
df1[[3]] - NULL
Best,
Ista
# Many thank's and with kind regards
Anna Zakrisson
º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•.
.• `•. .º
Anna Zakrisson Braeunlich
PhD student
Department of Ecology, Environment and Plant Sciences
Stockholm University
Svante Arrheniusv. 21A
SE-106 91 Stockholm
Sweden/Sverige
Lives in Berlin.
For paper mail:
Katzbachstr. 21
D-10965, Berlin
Germany/Deutschland
E-mail: anna.zakris...@su.se
Tel work: +49-(0)3091541281
Mobile: +49-(0)15777374888
LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
º`•. . • `•. .• `•. . º`•. . • `•. .• `•. .º`•. . • `•.
.• `•. .º
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.
I'm not sure I understood your problem, maybe like this: # split identifiers into columns df1 - data.frame(cbind(X = 1:10, Y = rnorm(10)), Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each = 5))) id - names(df1)[3] x - do.call(rbind, str_split(id, \\.)) y - sapply(x, function(z) z - df1[,id]) df1.goal - data.frame(df1[,-3], y) -dk -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Anna Zakrisson Braeunlich Gesendet: Sonntag, 12. Oktober 2014 09:25 An: r-help@r-project.org Betreff: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data. Hi, I have a question how to split a factor name into different columns. I have metabarcoding data and need to merge the FASTA-file with the taxonomy- and counttable files (dataframes). To be able to do this merge, I need to isolate the common identifier, that unfortunately is baked in with a lot of other labels in the factor name eg: sequence identifier: M01271_77_0.A8J0P_1_1101_10150_1525.1.322519.sample_1.sample_2 I want to split this name at every . to get several columns: column1: M01271_77_0 column2: A8J0P_1_1101_10150_1525 column3: 1 column4: 322519 column5: sample_1 column6: sample_2 I must add that I have no influence on how these names are given. This is how thay are supplied from Illumina Miseq. I just need to be able to deal with it. Here is some extremely simplified dummy data to further show the issue at hand: df1 - data.frame(cbind(X = 1:10, Y = rnorm(10)), Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each = 5))) df2 - data.frame(cbind(B = 13:22, K = rnorm(10)), Q.identifierA.B4668726 = factor(rep(LETTERS[1:2], each = 5))) # I have metabarcoding data with one FASTA-file, one count table and one taxonomy file # Above dummy data is just showing the issue at hand. I want to be able to merge my three # original data frames (here, the dummy data is only two dataframes). The problem is that # the only identifier that is commmon for the dataframes is hidden in the # factor name eg: Z.identifierA.1298712 and Q.identifierA.4668726. I hence need to be able # to split this name up into different columns to get identifierA alone as one column name # Then I can merge the dataframes. # How can I do this in R. I know that it can be done in excel, but I would like to # produce a complete R-script to get a fast pipeline and avoid copy and paste errors. # This is what I want it to look: df1.goal - data.frame(cbind(X = 1:10, Y = rnorm(10)), Z = factor(rep(LETTERS[1:2], each = 5)), identifierA = factor(rep(LETTERS[1:2], each = 5)), B1298712 = factor(rep(LETTERS[1:2], each = 5))) # Many thank's and with kind regards Anna Zakrisson ` . . ` . . ` . . ` . . ` . . ` . . ` . . ` . . ` . . Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin Germany/Deutschland E-mail: anna.zakris...@su.se Tel work: +49-(0)3091541281 Mobile: +49-(0)15777374888 LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b ` . . ` . . ` . . ` . . ` . . ` . . ` . . ` . . ` . . [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
