Sorry, I am pretty new using R.

Here is my code to read the table:

library("DESeq2")
setwd("~/Dropbox/TESIS/DGEA_2.0/Chapter_4_thesis/DE_analysis/DESeq2")
matrix = read.table (file.choose(), header=TRUE, row.names=1)
CeleDesign <- data.frame(
  row.names = colnames(matrix),
  condition = factor(c("SP", "SP", "EB", "EB")))
dds <- DESeqDataSetFromMatrix(countData = matrix,
                              colData = CeleDesign,
                              design = ~ condition)

By typing:

> setwd("~/Dropbox/TESIS/DGEA_2.0/Chapter_4_thesis/DE_analysis/DESeq2")
> setClass("NumerictoInteger")
> setAs("numeric", "NumerictoInteger", function(from) as.integer(from))
> matrix <- read.table(file.choose(), header=TRUE, , row.names=1,
stringsAsFactors=FALSE,
+ colClasses=c("character",rep("NumerictoInteger",11)))
Error in methods::as(data[[i]], colClasses[i]) :
  no method or default for coercing “character” to “NumerictoInteger”

My table has 12 columns and 138519 rows.
Any extra suggestion?

Thanks,
Alicia



--
Alicia R. Pérez-Porro
PhD candidate

Giribet lab
Department of Organismic and Evolutionary Biology
MCZ labs
Harvard University
26 Oxford St, Cambridge MA 02138
phone: +1 617-496-5308
fax: +1 617-495-5667
www.oeb.harvard.edu/faculty/giribet/

Department of Marine Ecology
Center for Advanced Studies of Blanes (CEAB-CSIC)
C/Accés Cala St. Francesc 14
17300 Blanes, Girona, SPAIN
phone: +34 972 336 101
fax: +34 972 337 806
www.ceab.csic.es


On Mon, May 12, 2014 at 9:57 PM, arun <smartpink111@yahoo.com> wrote:

> Hi,
>
> You may also try using 'colClasses' while reading the data.
> setClass("NumerictoInteger")
> setAs("numeric", "NumerictoInteger", function(from) as.integer(from))
> datx1 <- read.table(text=a, header=TRUE, stringsAsFactors=FALSE,
> colClasses=c("character",rep("NumerictoInteger",11)))
>
> ##David's result
>   dati <- data.frame(transcript_ID=datx$transcript_ID, sapply(datx[,-1],
> as.integer),
>          stringsAsFactors=FALSE)
>
>  all.equal(dati, datx1)
> #[1] TRUE
>
> A.K.
>
>
> On Monday, May 12, 2014 4:35 PM, David L Carlson <dcarlson@tamu.edu>
> wrote:
> a <- "transcript_ID C3 C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11 C1
> CRL_6OCT11c CRL_3DEC11  CRL_13DEC11b LRV_A LRV_B
> c101054_g1_i2 15.53 231.47 131.86 218.69 16.70 0.00 587.79 0.00 624.32
> 10.00 6.00
> c96583_g1_i2 0.00 10.60 6.30 8.87 0.00 0.00 29.00 0.00 90.94 0.00 0.00
> c19380_g1_i1 0.00 9.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c102980_g1_i10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c91905_g1_i3 0.00 6.66 65.11 0.00 0.00 0.00 40.92 0.00 55.37 0.00 0.00
> c108262_g1_i3 0.00 29.65 2.44 0.00 0.00 0.00 29.33 0.00 338.89 0.00 0.00
> c27948_g1_i1 0.00 0.00 0.00 54.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
> c14898_g1_i1 0.00 2.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c105146_g1_i2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00"
> datx <- read.table(text=a, header=TRUE, stringsAsFactors=FALSE)
>
> dati <- data.frame(datx$transcript_ID, sapply(datx[,-1], as.integer),
>         stringsAsFactors=FALSE)
>
> -------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77840-4352
>
>
> -----Original Message-----
> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> On Behalf Of Alicia R. Pérez-Porro
> Sent: Monday, May 12, 2014 10:38 AM
> To: r-help@r-project.org
> Subject: [R] Convert to integers all entries of a table (for DESeq2)
>
> Dear R users,
>
> I have a .txt table that looks like:
>
> transcript_ID C3        C4      CRL_2APR10      CRL_1_15JUL11
> CRL_2_15JUL11   C1      CRL_6OCT11c     CRL_3DEC11      CRL_13DEC11b
> LRV_A LRV_B
> c101054_g1_i2 15.53 231.47 131.86 218.69 16.70 0.00 587.79 0.00 624.32
> 10.00
> 6.00
> c96583_g1_i2 0.00 10.60 6.30 8.87 0.00 0.00 29.00 0.00 90.94 0.00 0.00
> c19380_g1_i1 0.00 9.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c102980_g1_i10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c91905_g1_i3 0.00 6.66 65.11 0.00 0.00 0.00 40.92 0.00 55.37 0.00 0.00
> c108262_g1_i3 0.00 29.65 2.44 0.00 0.00 0.00 29.33 0.00 338.89 0.00 0.00
> c27948_g1_i1 0.00 0.00 0.00 54.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
> c14898_g1_i1 0.00 2.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> c105146_g1_i2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
>
> I need to convert all the numeric entries into integers to be able to use
> DESeq2, e.g.:
>
> C3 C4 CRL2APR10 CRL_1_15JUL11 CRL_2_15JUL11 C1 CRL_6OCT11c CRL3DEC11
> CRL13DEC11b LRV_A LRV_B
> c101054_g1_i2 15 231 131 218 16 0 587 0 624 10 6
> c96583_g1_i2 0 10 6 8 0 0 29 0 90 0 0
> c19380_g1_i1 0 9 0 1 0 0 0 0 0 0 0
> c102980_g1_i10 0 0 0 0 0 0 0 0 0 0 0
> c91905_g1_i3 0 6 65 0 0 0 40 0 55 0 0
> c108262_g1_i3 0 29 2 0 0 0 29 0 338 0 0
> c27948_g1_i1 0 0 0 54 0 1 0 0 0 0 0
> c14898_g1_i1 0 2 0 1 0 0 0 0 0 0 0
> c105146_g1_i2 0 0 0 0 0 0 0 0 0 0 1
>
> ​Any help will be welcome.
> Thanks in advance,
>
> Alicia​
>
> --
> Alicia R. Pérez-Porro
> PhD candidate
>
> Giribet lab
> Department of Organismic and Evolutionary Biology
> MCZ labs
> Harvard University
> 26 Oxford St, Cambridge MA 02138
> phone: +1 617-496-5308
> fax: +1 617-495-5667
> www.oeb.harvard.edu/faculty/giribet/
>
> Department of Marine Ecology
> Center for Advanced Studies of Blanes (CEAB-CSIC)
> C/Accés Cala St. Francesc 14
> 17300 Blanes, Girona, SPAIN
> phone: +34 972 336 101
> fax: +34 972 337 806
> www.ceab.csic.es
>
>     [[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.
>

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