[BioC] Problem with chromLoc object.

[Furge, Kyle]

Thanks for the report and the example. The package maintainer is on summer holiday for the next few days so there may be a delay in his reply.

I think you can manually specify the chromosome names using the "chr" argument in the cset2band() function call.  The syntax will be a bit confusing because in your example "chr" is also the variable name for the chromLoc object.

banded <- cset2band(exprs=exprs,genome=chr,chr=c(1:22,"X","Y"),FUN=mean,na.rm=TRUE)

This will hopefully bypass the more cryptic names in the chromLoc object and help move the process along.

-kyle


On 6/24/10 3:58 PM, "Sathe, Tejas" <sathet at ccf.org> wrote:

I am having a problem with the chromLoc object while trying to use the cset2band method in the reb package. I am trying to do a genome wide cytogenic analysis.

Here is my full code.

library(affy)
library(hgu133plus2.db)
library(hgu133plus2barcodevecs)
library(hgu133plus2cdf)
library(idiogram)
library(reb)

expr <- justRMA()

matrix <- assayData(expr)$exprs

#Define oncocytoma as norms
norms <- 16:30


chr <- buildChromLocation.2("hgu133plus2.db","bands")

cset <- reb(matrix,chr,ref=norms,center=TRUE)

exprs <- cset[,-norms]
exprs[abs(exprs) < 1.96] <- NA

banded <- cset2band(exprs,chr,FUN=mean,na.rm=TRUE)

h.cyto <- buildChromCytoband(organism = "h")

midiogram(banded,h.cyto,method="i",col=.rwb,dlim=c(-4,4))

This is based off of the reference manual for the reb package.

At the cset2band line, I get the following error:
Error in get(chr, cytoEnv) : object '6_ssto_hap7' not found

I believe this is due to the fact that my chr object contains additional chromosomes and I'm not sure how to deal with them.

contents of chr:

Instance of a chromLocation class with the following fields:
        Organism:  Homo sapiens
        Data source:  hgu133plus2.db
        Number of chromosomes for this organism:  93
        Chromosomes of this organism and their lengths in base pairs:
                 1 : 249250621
                 2 : 243199373
                 3 : 198022430
                 4 : 191154276
                 5 : 180915260
                 6 : 171115067
                 7 : 159138663
                 X : 155270560
                 8 : 146364022
                 9 : 141213431
                 10 : 135534747
                 11 : 135006516
                 12 : 133851895
                 13 : 115169878
                 14 : 107349540
                 15 : 102531392
                 16 : 90354753
                 17 : 81195210
                 18 : 78077248
                 20 : 63025520
                 Y : 59373566
                 19 : 59128983
                 22 : 51304566
                 21 : 48129895
                 6_ssto_hap7 : 4928567
                 6_mcf_hap5 : 4833398
                 6_cox_hap2 : 4795371
                 6_mann_hap4 : 4683263
                 6_apd_hap1 : 4622290
                 6_qbl_hap6 : 4611984
                 6_dbb_hap3 : 4610396
                 17_ctg5_hap1 : 1680828
                 4_ctg9_hap1 : 590426
                 1_gl000192_random : 547496
                 Un_gl000225 : 211173
                 4_gl000194_random : 191469
                 4_gl000193_random : 189789
                 9_gl000200_random : 187035
                 Un_gl000222 : 186861
                 Un_gl000212 : 186858
                 7_gl000195_random : 182896
                 Un_gl000223 : 180455
                 Un_gl000224 : 179693
                 Un_gl000219 : 179198
                 17_gl000205_random : 174588
                 Un_gl000215 : 172545
                 Un_gl000216 : 172294
                 Un_gl000217 : 172149
                 9_gl000199_random : 169874
                 Un_gl000211 : 166566
                 Un_gl000213 : 164239
                 Un_gl000220 : 161802
                 Un_gl000218 : 161147
                 19_gl000209_random : 159169
                 Un_gl000221 : 155397
                 Un_gl000214 : 137718
                 Un_gl000228 : 129120
                 Un_gl000227 : 128374
                 1_gl000191_random : 106433
                 19_gl000208_random : 92689
                 9_gl000198_random : 90085
                 17_gl000204_random : 81310
                 Un_gl000233 : 45941
                 Un_gl000237 : 45867
                 Un_gl000230 : 43691
                 Un_gl000242 : 43523
                 Un_gl000243 : 43341
                 Un_gl000241 : 42152
                 Un_gl000236 : 41934
                 Un_gl000240 : 41933
                 17_gl000206_random : 41001
                 Un_gl000232 : 40652
                 Un_gl000234 : 40531
                 11_gl000202_random : 40103
                 Un_gl000238 : 39939
                 Un_gl000244 : 39929
                 Un_gl000248 : 39786
                 8_gl000196_random : 38914
                 Un_gl000249 : 38502
                 Un_gl000246 : 38154
                 17_gl000203_random : 37498
                 8_gl000197_random : 37175
                 Un_gl000245 : 36651
                 Un_gl000247 : 36422
                 9_gl000201_random : 36148
                 Un_gl000235 : 34474
                 Un_gl000239 : 33824
                 21_gl000210_random : 27682
                 Un_gl000231 : 27386
                 Un_gl000229 : 19913
                 M : 16571
                 Un_gl000226 : 15008
                 18_gl000207_random : 4262
>

Thanks,

Tejas

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