methylkit correlation unite min.per.group NA

Linda Molla

unread,

Oct 21, 2017, 10:29:02 PM10/21/17

to methylkit_...@googlegroups.com

I am using the function below

#for the CpG site to be considered it has to be covered in at least 3 out of 5 BR

meth = unite(myobj,min.per.group=3L)

and then

getCorrelation(meth, plot = FALSE)

The correlation table value I get has NA values.

I am wondering why is this happening/ what am I doing wrong.

Linda

_______________

table:

G_d1 G_2 G_3 G_4 G_5 A_1 A_d2 A_3 A_4 A_5

G_1 1 NA NA NA NA NA NA NA NA NA

G_2 NA 1 NA NA NA NA NA NA NA NA

G_3 NA NA 1 NA NA NA NA NA NA NA

G_4 NA NA NA 1 NA NA NA NA NA NA

G_5 NA NA NA NA 1 NA NA NA NA NA

A_1 NA NA NA NA NA 1 NA NA NA NA

A_2 NA NA NA NA NA NA 1 NA NA NA

A_3 NA NA NA NA NA NA NA 1 NA NA

A_4 NA NA NA NA NA NA NA NA 1 NA

A_5 NA NA NA NA NA NA NA NA NA 1

Altuna Akalin

unread,

Oct 25, 2017, 8:43:33 AM10/25/17

to methylkit_...@googlegroups.com

don't use min.per.group when you want to check correlation between samples, that should resolve it. NA values in methyKit objects creates a problem for the correlation function, although this could be fixed, we never got around to it.

Best,

Altuna

--
You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.
To post to this group, send email to methylkit_discussion@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

Linda Molla

unread,

Oct 31, 2017, 4:22:09 PM10/31/17

to methylkit_discussion

Related to the above error most likely

I am trying to run regionCounts on the meth object above, which contains NA(s). And it throws an error at the calculateDiffMeth step.

meth = unite(myobj,min.per.group=3L)

methfeature=regionCounts(meth,genomicfeature,cov.bases = 3)

myDifffeatrure = calculateDiffMeth(methfeature, num.cores = 4)

Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :

0 (non-NA) cases

In addition: Warning messages:

1: glm.fit: fitted probabilities numerically 0 or 1 occurred

2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

To post to this group, send email to methylkit_...@googlegroups.com.

Altuna Akalin

unread,

Nov 1, 2017, 3:17:59 AM11/1/17

to methylkit_...@googlegroups.com

This could be sth else, please send a reproducible example

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discus...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.

Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discus...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--

Sent from mobile, excuse the brevity

Linda Molla

unread,

Nov 1, 2017, 6:01:21 PM11/1/17

to methylkit_discussion

Ran this with the example of the vignette and a different error shows up

file.list=list( system.file("extdata", "test1.myCpG.txt", package = "methylKit"),

+ system.file("extdata", "test2.myCpG.txt", package = "methylKit"),

+ system.file("extdata", "control1.myCpG.txt", package = "methylKit"),

+ system.file("extdata", "control2.myCpG.txt", package = "methylKit") )

myobj=methRead( file.list, sample.id=list("test1","test2","ctrl1","ctrl2"),assembly="hg18",treatment=c(1,1,0,0))

filtered.myobj=filterByCoverage(myobj,lo.count=10,lo.perc=NULL,

hi.count=NULL,hi.perc=99.9)

meth=unite(filtered.myobj, destrand=TRUE,min.per.group=1L)

myDiffFiltered = getMethylDiff(myDiff)

gene.obj=readTranscriptFeatures(system.file("extdata", "refseq.hg18.bed.txt",

package = "methylKit"))

promoters=regionCounts(meth,gene.obj$promoters,cov.bases = 3)

> myDiffpromoters = calculateDiffMeth(promoters, num.cores = 4)

Error in if (any(y < 0 | y > 1)) stop("y values must be 0 <= y <= 1") :

missing value where TRUE/FALSE needed

______

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Mavericks 10.9.5

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:

[1] TxDb.Mmusculus.UCSC.mm10.ensGene_3.2.2 GenomicFeatures_1.24.5

[3] AnnotationDbi_1.34.4 Biobase_2.32.0

[5] BiocInstaller_1.22.3 bindrcpp_0.2

[7] dplyr_0.7.4 reshape2_1.4.2

[9] ggplot2_2.2.1 edmr_0.6.4.1

[11] devtools_1.13.3 methylKit_0.99.2

[13] genomation_1.4.2 GenomicRanges_1.24.3

[15] GenomeInfoDb_1.8.7 IRanges_2.6.1

[17] S4Vectors_0.10.3 BiocGenerics_0.18.0

[19] biomaRt_2.28.0

loaded via a namespace (and not attached):

[1] mixtools_1.1.0 httr_1.3.1 bit64_0.9-7 splines_3.3.3

[5] R.utils_2.5.0 gtools_3.5.0 assertthat_0.2.0 blob_1.1.0

[9] BSgenome_1.40.1 Rsamtools_1.24.0 impute_1.46.0 numDeriv_2016.8-1

[13] RSQLite_2.0 lattice_0.20-35 glue_1.2.0 limma_3.28.21

[17] bbmle_1.0.20 digest_0.6.12 XVector_0.12.1 qvalue_2.4.2

[21] colorspace_1.3-2 Matrix_1.2-11 R.oo_1.21.0 plyr_1.8.4

[25] pkgconfig_2.0.1 XML_3.98-1.9 emdbook_1.3.9 zlibbioc_1.18.0

[29] scales_0.5.0 BiocParallel_1.6.6 git2r_0.19.0 tibble_1.3.4

[33] seqPattern_1.4.0 withr_2.0.0 SummarizedExperiment_1.2.3 lazyeval_0.2.1

[37] survival_2.41-3 magrittr_1.5 mclust_5.3 memoise_1.1.0

[41] R.methodsS3_1.7.1 MASS_7.3-47 segmented_0.5-2.2 tools_3.3.3

[45] data.table_1.10.4-3 hms_0.3 matrixStats_0.52.2 gridBase_0.4-7

[49] stringr_1.2.0 munsell_0.4.3 plotrix_3.6-6 Biostrings_2.40.2

[53] fastseg_1.18.0 rlang_0.1.2 RCurl_1.95-4.8 labeling_0.3

[57] bitops_1.0-6 gtable_0.2.0 DBI_0.7 curl_3.0

[61] R6_2.2.2 GenomicAlignments_1.8.4 knitr_1.17 rtracklayer_1.32.2

[65] bit_1.1-12 bindr_0.1 KernSmooth_2.23-15 readr_1.1.1

[69] stringi_1.1.5 Rcpp_0.12.13 coda_0.19-1

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.

Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

Altuna Akalin

unread,

Nov 2, 2017, 5:10:10 AM11/2/17

to methylkit_...@googlegroups.com

can you update your methylKit to the latest version and retry your example, this might have been fixed in the latest version:

https://github.com/al2na/methylKit/pull/77. Let me know how it goes

library(devtools)
install_github("al2na/methylKit", build_vignettes=FALSE, 
  repos=BiocInstaller::biocinstallRepos(),
  dependencies=TRUE)

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsubscrib...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.

Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsubscrib...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--
Sent from mobile, excuse the brevity

--

You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.

To post to this group, send email to methylkit_discussion@googlegroups.com.

Linda Molla

unread,

Nov 9, 2017, 3:05:43 PM11/9/17

to methylkit_discussion

Sorry for the delay,

With the new version this error does not show up anymore

methylKit_1.3.8

R version 3.4.2

thanks

> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 16.04.3 LTS

Matrix products: default

BLAS: /usr/local/lib/R/lib/libRblas.so

LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8

[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] grid parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:

[1] bindrcpp_0.2 devtools_1.13.3 dplyr_0.7.4 reshape2_1.4.2 ggplot2_2.2.1 genomation_1.8.0 biomaRt_2.32.1

[8] edmr_0.6.4.1 methylKit_1.3.8 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7 BiocGenerics_0.22.1

loaded via a namespace (and not attached):

[1] Biobase_2.36.2 mixtools_1.1.0 bit64_0.9-7 splines_3.4.2 R.utils_2.5.0

[6] gtools_3.5.0 assertthat_0.2.0 blob_1.1.0 BSgenome_1.44.2 GenomeInfoDbData_0.99.0

[11] Rsamtools_1.28.0 yaml_2.1.14 impute_1.50.1 numDeriv_2016.8-1 RSQLite_2.0

[16] lattice_0.20-35 glue_1.2.0 limma_3.32.10 bbmle_1.0.20 digest_0.6.12

[21] XVector_0.16.0 qvalue_2.8.0 colorspace_1.3-2 Matrix_1.2-11 R.oo_1.21.0

[26] plyr_1.8.4 pkgconfig_2.0.1 XML_3.98-1.9 emdbook_1.3.9 zlibbioc_1.22.0

[31] scales_0.5.0 BiocParallel_1.10.1 tibble_1.3.4 withr_2.1.0 seqPattern_1.8.0

[36] SummarizedExperiment_1.6.5 lazyeval_0.2.1 survival_2.41-3 magrittr_1.5 mclust_5.3

[41] memoise_1.1.0 R.methodsS3_1.7.1 MASS_7.3-47 segmented_0.5-2.2 tools_3.4.2

[46] data.table_1.10.4-3 hms_0.3 matrixStats_0.52.2 gridBase_0.4-7 stringr_1.2.0

[51] munsell_0.4.3 plotrix_3.6-6 DelayedArray_0.2.7 AnnotationDbi_1.38.2 Biostrings_2.44.2

[56] compiler_3.4.2 fastseg_1.22.0 rlang_0.1.2 RCurl_1.95-4.8 labeling_0.3

[61] bitops_1.0-6 gtable_0.2.0 DBI_0.7 R6_2.2.2 GenomicAlignments_1.12.2

[66] rtracklayer_1.36.6 bit_1.1-12 bindr_0.1 KernSmooth_2.23-15 readr_1.1.1

[71] stringi_1.1.5 Rcpp_0.12.13 coda_0.19-1

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.

To post to this group, send email to methylkit_...@googlegroups.com.

Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.
To post to this group, send email to methylkit_...@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

--
Sent from mobile, excuse the brevity

--

You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discussion+unsub...@googlegroups.com.

Reply all

Reply to author

Forward