Hi,
I remember I got the same error when I used:
setAs("numeric", "NumerictoInteger", function(from) as.integer(from))
##Using the same dataset
datx1 <- read.table(text=a, header=TRUE, 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”
#Changing "numeric" to "character" gives me:
setAs("character", "NumerictoInteger", function(from) as.integer(from))
##though
datx1 <- read.table(text=a, header=TRUE, stringsAsFactors=FALSE,
colClasses=c("character",rep("NumerictoInteger",11)))
str(datx1)
'data.frame': 9 obs. of 12 variables:
$ transcript_ID: chr "c101054_g1_i2" "c96583_g1_i2" "c19380_g1_i1"
"c102980_g1_i10" ...
$ C3 : int 15 0 0 0 0 0 0 0 0
$ C4 : int 231 10 9 0 6 29 0 2 0
$ CRL_2APR10 : int 131 6 0 0 65 2 0 0 0
$ CRL_1_15JUL11: int 218 8 1 0 0 0 54 1 0
$ CRL_2_15JUL11: int 16 0 0 0 0 0 0 0 0
$ C1 : int 0 0 0 0 0 0 1 0 0
$ CRL_6OCT11c : int 587 29 0 0 40 29 0 0 0
$ CRL_3DEC11 : int 0 0 0 0 0 0 0 0 0
$ CRL_13DEC11b : int 624 90 0 0 55 338 0 0 0
$ LRV_A : int 10 0 0 0 0 0 0 0 0
$ LRV_B : int 6 0 0 0 0 0 0 0 1
A.K.
On Wednesday, May 14, 2014 2:46 PM, Alicia R. Pérez-Porro
<alicia.r.perezpo...@gmail.com> wrote:
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 <smartpink...@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$transcript_ID, sapply(datx[,-1],
>as.integer),
> stringsAsFactors=FALSE)
>
> all.equal(dati, datx1)
>#[1] TRUE
>
>A.K.
>
>
>
>On Monday, May 12, 2014 4:35 PM, David L Carlson <dcarl...@tamu.edu> wrote:
>a <- "transcript_ID C3 C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11 C1
>CRL_6OCT11c CRL_3DEC11 CRL_13DEC11b LRV_A LRV_B
>c101054_g1_i2 15.53 231.47 131.86 218.69 16.70 0.00 587.79 0.00 624.32 10.00
>6.00
>c96583_g1_i2 0.00 10.60 6.30 8.87 0.00 0.00 29.00 0.00 90.94 0.00 0.00
>c19380_g1_i1 0.00 9.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>c102980_g1_i10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>c91905_g1_i3 0.00 6.66 65.11 0.00 0.00 0.00 40.92 0.00 55.37 0.00 0.00
>c108262_g1_i3 0.00 29.65 2.44 0.00 0.00 0.00 29.33 0.00 338.89 0.00 0.00
>c27948_g1_i1 0.00 0.00 0.00 54.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
>c14898_g1_i1 0.00 2.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>c105146_g1_i2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00"
>datx <- read.table(text=a, header=TRUE, stringsAsFactors=FALSE)
>
>dati <- data.frame(datx$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-boun...@r-project.org [mailto:r-help-boun...@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]]
>
>______________________________________________
>R-help@r-project.org mailing list
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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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