[Bioc-devel] requirement for named assays in SummarizedExperiment

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

 > assays(se1)

List of length 1
names(1): counts1

 > assays(se2)

List of length 1
names(1): counts2

 > cbind(se1, se2)

Error in sQuote(accessorName) :
   argument "accessorName" is missing, with no default


Valerie


On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)
nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()

R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

Hi,

After talking with others the vote was against enforcing names on assays()
and for positional matching if all names are NULL. A mixture of names and
NULL throws an error.

example(SummarizedExperiment)

## all named

se2 = se1
assays(cbind(se1, se2))

List of length 1
names(1): counts

## mixture of names and NULL -> error

names(assays(se1)) = NULL
assays(cbind(se1, se2))

Error in assays(cbind(se1, se2)) :
  error in evaluating the argument 'x' in selecting a method for function
'assays': Error in .bind.arrays(args, cbind, "assays") :
  elements in ?assays? must have the same names

## all NULL -> positional matching

names(assays(se2)) = NULL
assays(cbind(se1, se2))

List of length 1

If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.

Changes are in 1.19.46.

Valerie




On 03/06/2015 08:20 AM, Valerie Obenchain wrote:

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

 > assays(se1)

List of length 1
names(1): counts1

 > assays(se2)

List of length 1
names(1): counts2

 > cbind(se1, se2)

Error in sQuote(accessorName) :
   argument "accessorName" is missing, with no default


Valerie


On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

 require(GenomicRanges)

nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

 sessionInfo()

R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fredhutch.org
Phone: (206) 667-3158

On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear there is
an order of the assays.

On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:

Hi,

After talking with others the vote was against enforcing names on assays()
and for positional matching if all names are NULL. A mixture of names and
NULL throws an error.

example(SummarizedExperiment)

## all named

se2 = se1
assays(cbind(se1, se2))

List of length 1
names(1): counts

## mixture of names and NULL -> error

names(assays(se1)) = NULL
assays(cbind(se1, se2))

Error in assays(cbind(se1, se2)) :
 error in evaluating the argument 'x' in selecting a method for function
'assays': Error in .bind.arrays(args, cbind, "assays") :
 elements in ?assays? must have the same names

## all NULL -> positional matching

names(assays(se2)) = NULL
assays(cbind(se1, se2))

List of length 1

If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.

Changes are in 1.19.46.

Valerie

On 03/06/2015 08:20 AM, Valerie Obenchain wrote:

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

assays(se1)

List of length 1
names(1): counts1

assays(se2)

List of length 1
names(1): counts2

cbind(se1, se2)

Error in sQuote(accessorName) :
  argument "accessorName" is missing, with no default


Valerie

On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)

nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()
R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fredhutch.org
Phone: (206) 667-3158

   [[alternative HTML version deleted]]

What he said

This doesn't make any sense from an API perspective.  When would a user ever expect to see unnamed assay matrices?

--t

On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear there is
an order of the assays.

On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:

Hi,

After talking with others the vote was against enforcing names on assays()
and for positional matching if all names are NULL. A mixture of names and
NULL throws an error.

example(SummarizedExperiment)

## all named

se2 = se1
assays(cbind(se1, se2))

List of length 1
names(1): counts

## mixture of names and NULL -> error

names(assays(se1)) = NULL
assays(cbind(se1, se2))

Error in assays(cbind(se1, se2)) :
  error in evaluating the argument 'x' in selecting a method for function
'assays': Error in .bind.arrays(args, cbind, "assays") :
  elements in ?assays? must have the same names

## all NULL -> positional matching

names(assays(se2)) = NULL
assays(cbind(se1, se2))

List of length 1

If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.

Changes are in 1.19.46.

Valerie

On 03/06/2015 08:20 AM, Valerie Obenchain wrote:

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

assays(se1)

List of length 1
names(1): counts1

assays(se2)

List of length 1
names(1): counts2

cbind(se1, se2)

Error in sQuote(accessorName) :
   argument "accessorName" is missing, with no default


Valerie

On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)

nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()
R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fredhutch.org
Phone: (206) 667-3158

    [[alternative HTML version deleted]]

On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:

What he said

This doesn't make any sense from an API perspective.  When would a 
user ever expect to see unnamed assay matrices?

When there's a single assay?

--t

On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen 
<kasperdanielhansen at gmail.com> wrote:

allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear 
there is
an order of the assays.

On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain 
<vobencha at fredhutch.org>
wrote:

Hi,

After talking with others the vote was against enforcing names on 
assays()
and for positional matching if all names are NULL. A mixture of 
names and
NULL throws an error.

example(SummarizedExperiment)

## all named

se2 = se1
assays(cbind(se1, se2))

List of length 1
names(1): counts

## mixture of names and NULL -> error

names(assays(se1)) = NULL
assays(cbind(se1, se2))

Error in assays(cbind(se1, se2)) :
  error in evaluating the argument 'x' in selecting a method for 
function
'assays': Error in .bind.arrays(args, cbind, "assays") :
  elements in ?assays? must have the same names

## all NULL -> positional matching

names(assays(se2)) = NULL
assays(cbind(se1, se2))

List of length 1

If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.

Changes are in 1.19.46.

Valerie

On 03/06/2015 08:20 AM, Valerie Obenchain wrote:

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone 
is too
dangerous. I'm thinking of the VCF class where the genome 
information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

assays(se1)

List of length 1
names(1): counts1

assays(se2)

List of length 1
names(1): counts2

cbind(se1, se2)

Error in sQuote(accessorName) :
   argument "accessorName" is missing, with no default


Valerie

On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)

nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, 
colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think 
this is
due to the fact that the cbind code matches up assays by their 
names.
Thus, if there are no names, the code assumes that there are no 
assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be 
modified
to work positionally when there are no assay names, e.g., by 
cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()
R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13 IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fredhutch.org
Phone: (206) 667-3158

    [[alternative HTML version deleted]]

On Mar 12, 2015, at 9:24 AM, Martin Morgan <mtmorgan at fredhutch.org> wrote:

On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said

This doesn't make any sense from an API perspective.  When would a user ever expect to see unnamed assay matrices?

When there's a single assay?

--t

On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear there is
an order of the assays.

On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:

Hi,

After talking with others the vote was against enforcing names on assays()
and for positional matching if all names are NULL. A mixture of names and
NULL throws an error.

example(SummarizedExperiment)

## all named

se2 = se1
assays(cbind(se1, se2))

List of length 1
names(1): counts

## mixture of names and NULL -> error

names(assays(se1)) = NULL
assays(cbind(se1, se2))

Error in assays(cbind(se1, se2)) :
 error in evaluating the argument 'x' in selecting a method for function
'assays': Error in .bind.arrays(args, cbind, "assays") :
 elements in ?assays? must have the same names

## all NULL -> positional matching

names(assays(se2)) = NULL
assays(cbind(se1, se2))

List of length 1

If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.

Changes are in 1.19.46.

Valerie

On 03/06/2015 08:20 AM, Valerie Obenchain wrote:

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

assays(se1)

List of length 1
names(1): counts1

assays(se2)

List of length 1
names(1): counts2

cbind(se1, se2)

Error in sQuote(accessorName) :
  argument "accessorName" is missing, with no default


Valerie

On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)

nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()
R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4

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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fredhutch.org
Phone: (206) 667-3158

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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793