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LambdaSets converting the results into a data.frame

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joe j ▴ 70

@joe-j-4637

Last seen 10.2 years ago

Dear all, This is probably a simple question, but any pointers would be great. I am using "lambdaSets" in the package "RBGL" in R. What I would like is to have all the results of "lambdaSets" in a data.frame because I will be comparing the results for different years. Best regards, Joe

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ADD COMMENT • link updated 13.6 years ago by Steve Lianoglou ★ 13k • written 13.6 years ago by joe j ▴ 70

score 0 · Answer 1 · 2011-05-16

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

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Hi, On Mon, May 16, 2011 at 4:29 AM, joe j <joe.stata at="" gmail.com=""> wrote: > Dear all, > > This is probably a simple question, but any pointers would be great. > > I am using ?"lambdaSets" in the package "RBGL" in R. What I would like > is to have all the results of "lambdaSets" in a data.frame because I > will be comparing the results for different years. How do you expect that data.frame to look like? For instance, if we run the example code in the lambdaSets function and set the last statement to a variable (`lset`): R> con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) R> coex <- fromGXL(con) R> close(con) R> lset <- lambdaSets(coex) What do you expect `lset` as a data.frame to look like? lset[[1]] is a single integer, and lset[[2]] is a list of lists of nodes -- each of varying lengths. It seems that this type of data isn't well suited to be stuffed into a data.frame, but if you can give us an idea of how this `lset` object might look like as a data.frame, perhaps someone can help you get it into that form. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 13.6 years ago Steve Lianoglou ★ 13k

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Thanks, Steve, What I've in mind is essentially a matrix of 3 columns: 1.vertex label, 2. edge connectivity (from 1 to maximum edge connectivity) or let's call it Lambda-K-set,3. a lambda set group identifier; let's call it group For the example: con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) coex <- fromGXL(con) close(con) lambdaSets(coex) I'd like the following output: 1. Node; 2. Lambda-K-set; 3. Group A1 1 1 A2 1 1 -- A12 1 1 A1 2 1 A2 2 1 -- A8 2 1 A9 2 2 A10 2 2 -- A12 2 2 A1 3 1 A2 3 1 -- A4 3 1 A5 3 2 A6 3 2 -- A8 3 2 Best regards, Joe On Mon, May 16, 2011 at 3:50 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Mon, May 16, 2011 at 4:29 AM, joe j <joe.stata at="" gmail.com=""> wrote: >> Dear all, >> >> This is probably a simple question, but any pointers would be great. >> >> I am using ?"lambdaSets" in the package "RBGL" in R. What I would like >> is to have all the results of "lambdaSets" in a data.frame because I >> will be comparing the results for different years. > > How do you expect that data.frame to look like? > > For instance, if we run the example code in the lambdaSets function > and set the last statement to a variable (`lset`): > > R> con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) > R> coex <- fromGXL(con) > R> close(con) > R> lset <- lambdaSets(coex) > > What do you expect `lset` as a data.frame to look like? > > lset[[1]] is a single integer, and lset[[2]] is a list of lists of > nodes -- each of varying lengths. It seems that this type of data > isn't well suited to be stuffed into a data.frame, but if you can give > us an idea of how this `lset` object might look like as a data.frame, > perhaps someone can help you get it into that form. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact >

ADD REPLY • link 13.6 years ago joe j ▴ 70

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Hi, On Mon, May 16, 2011 at 11:18 AM, joe j <joe.stata at="" gmail.com=""> wrote: > Thanks, Steve, > What I've in mind is essentially a matrix of 3 columns: > 1.vertex label, 2. edge connectivity (from 1 to maximum edge > connectivity) or let's call it Lambda-K-set,3. a lambda set group > identifier; let's call it group > > For the example: > ?con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) > ?coex <- fromGXL(con) > ?close(con) > ?lambdaSets(coex) > > I'd like the following output: > > 1. Node; 2. Lambda-K-set; 3. Group > > A1 ? ? ? ?1 ? ? ? ?1 > A2 ? ? ? ?1 ? ? ? ?1 > -- > A12 ? ? ?1 ? ? ? ?1 > > > A1 ? ? ? ?2 ? ? ? ?1 > A2 ? ? ? ?2 ? ? ? ?1 > -- > A8 ? ? ? ?2 ? ? ? ?1 > > A9 ? ? ? ?2 ? ? ? 2 > A10 ? ? ?2 ? ? ? 2 > -- > A12 ? ? ?2 ? ? ? 2 > > > A1 ? ? ? 3 ? ? ? 1 > A2 ? ? ? 3 ? ? ? 1 > -- > A4 ? ? ? 3 ? ? ? 1 > > > A5 ? ? ?3 ? ? ? 2 > A6 ? ? ?3 ? ? ? 2 > -- > A8 ? ? ?3 ? ? ? 2 Here's a way -- maybe not the prettiest, but I think it's (more or less) what you're after. The `lsets` variable should have. The parse* functions may not be so durable/robust, and might require tweaking: library(RGDL) con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) coex <- fromGXL(con) close(con) lset <- lambdaSets(coex) parse.me <- unlist(lset[[2]], recursive=FALSE) parseLambda <- function(name) { gsub('lambda-(\\d+).*', '\\1', name) } parseSet <- function(name) { idx <- gsub('lambda-(\\d+) sets(\\d+)', '\\2', name) if (nchar(idx) == nchar(name)) { ## idx not found, assume 1 idx <- "1" } idx } lsets <- lapply(namesparse.me), function(name) { lambda <- parseLambda(name) group <- parseSet(name) data.frame(node=parse.me[[name]], lambda=lambda, group=group) }) lsets <- do.call(rbind, lsets) head(lsets) node lambda group 1 A1 0 1 2 A2 0 1 3 A3 0 1 4 A4 0 1 5 A5 0 1 6 A6 0 1 -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 13.6 years ago Steve Lianoglou ★ 13k

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Thanks very much Steve. Just what I wanted. Joe On Mon, May 16, 2011 at 5:56 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Mon, May 16, 2011 at 11:18 AM, joe j <joe.stata at="" gmail.com=""> wrote: >> Thanks, Steve, >> What I've in mind is essentially a matrix of 3 columns: >> 1.vertex label, 2. edge connectivity (from 1 to maximum edge >> connectivity) or let's call it Lambda-K-set,3. a lambda set group >> identifier; let's call it group >> >> For the example: >> ?con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) >> ?coex <- fromGXL(con) >> ?close(con) >> ?lambdaSets(coex) >> >> I'd like the following output: >> >> 1. Node; 2. Lambda-K-set; 3. Group >> >> A1 ? ? ? ?1 ? ? ? ?1 >> A2 ? ? ? ?1 ? ? ? ?1 >> -- >> A12 ? ? ?1 ? ? ? ?1 >> >> >> A1 ? ? ? ?2 ? ? ? ?1 >> A2 ? ? ? ?2 ? ? ? ?1 >> -- >> A8 ? ? ? ?2 ? ? ? ?1 >> >> A9 ? ? ? ?2 ? ? ? 2 >> A10 ? ? ?2 ? ? ? 2 >> -- >> A12 ? ? ?2 ? ? ? 2 >> >> >> A1 ? ? ? 3 ? ? ? 1 >> A2 ? ? ? 3 ? ? ? 1 >> -- >> A4 ? ? ? 3 ? ? ? 1 >> >> >> A5 ? ? ?3 ? ? ? 2 >> A6 ? ? ?3 ? ? ? 2 >> -- >> A8 ? ? ?3 ? ? ? 2 > > Here's a way -- maybe not the prettiest, but I think it's (more or > less) what you're after. The `lsets` variable should have. The parse* > functions may not be so durable/robust, and might require tweaking: > > library(RGDL) > > con <- file(system.file("XML/snalambdaex.gxl",package="RBGL")) > coex <- fromGXL(con) > close(con) > lset <- lambdaSets(coex) > > parse.me <- unlist(lset[[2]], recursive=FALSE) > > parseLambda <- function(name) { > ?gsub('lambda-(\\d+).*', '\\1', name) > } > > parseSet <- function(name) { > ?idx <- gsub('lambda-(\\d+) sets(\\d+)', '\\2', name) > ?if (nchar(idx) == nchar(name)) { > ? ?## idx not found, assume 1 > ? ?idx <- "1" > ?} > ?idx > } > > lsets <- lapply(namesparse.me), function(name) { > ?lambda <- parseLambda(name) > ?group <- parseSet(name) > ?data.frame(node=parse.me[[name]], lambda=lambda, group=group) > }) > > lsets <- do.call(rbind, lsets) > > head(lsets) > ?node lambda group > 1 ? A1 ? ? ?0 ? ? 1 > 2 ? A2 ? ? ?0 ? ? 1 > 3 ? A3 ? ? ?0 ? ? 1 > 4 ? A4 ? ? ?0 ? ? 1 > 5 ? A5 ? ? ?0 ? ? 1 > 6 ? A6 ? ? ?0 ? ? 1 > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact >

ADD REPLY • link 13.6 years ago joe j ▴ 70