DoOR consists of two R packages and both are needed for DoOR to work properly. One package, DoOR.data contains all the Drosophila odor responses we gathered from labs around the world or recorded ourselves. The other package DoOR.functions contains the DoOR framework for integrating heterogeneous data sets as well as analysis tools and functions for visualization.

In this vignette we describe how to build, modify and update DoOR and introduce some helper functions. There are two other vignettes explaining the plotting functions and the analysis tools in detail. ##

The first step after starting R is to attach both packages and to load the response data:

library(DoOR.data)
library(DoOR.functions)
loadData()

loadData() attaches the data from DoOR.data.

# Modifying, building and updating DoOR

DoOR comes with all the original data sets as well as with a pre-computed version of the consensus matrix response.matrix where all data was integrated using the DoOR merging algorithms (see paper for details on how the algorithm works). The values in response.matrix are globally normalized with values scaled [0,1]. response.matrix_non.normalized is a version of the consensus data that is not globally normalized meaning that responses are scaled [0,1] within each responding unit (receptor, sensory neuron, glomerulus…).

## Importing new data with importNewData()

It is easy to add new response data to DoOR, we only have to take care to provide it in the right format:

• either a .csv or a .txt file with fields separated by colons or tabs (see ?read.table for detailed specifications).
• the filename corresponds to the later name of the data set
• if we add e.g. recordings obtained with different methods, these should go into two data sets and thus into two different files that we import
• e.g. “Hallem.2004.EN” and “Hallem.2004.WT” are the “empty neuron” and the “wildtype neuron” recordings from Elissa Hallem’s 2004 publication
• the file needs at least two columns:
1. one column named “InChIKey” holding the InChIKey of the odorant
2. one column named after the responding unit the recording comes from (e.g. “Or22a”)

A minimal example file could look like this:

InChIKey Or22a
1 SFR 4
3 VHUUQVKOLVNVRT-UHFFFAOYSA-N 17
4 KIDHWZJUCRJVML-UHFFFAOYSA-N 16
5 VHRGRCVQAFMJIZ-UHFFFAOYSA-N 17

We can provide more chemical identifiers:

Class Name InChIKey CID CAS Or22a
1 NA sfr SFR SFR SFR 4
3 amine ammonium hydroxide VHUUQVKOLVNVRT-UHFFFAOYSA-N 14923 1336-21-6 17
4 amine putrescine KIDHWZJUCRJVML-UHFFFAOYSA-N 1045 110-60-1 16
5 amine cadaverine VHRGRCVQAFMJIZ-UHFFFAOYSA-N 273 462-94-2 17

Any of the following will be imported:

Class : e.g. “ester” : the chemical class an odorant belongs to

Name : e.g. “isopentyl acetate”

InChIKey : e.g. “MLFHJEHSLIIPHL-UHFFFAOYSA-N” (details)

InChI : e.g. “InChI=1S/C7H14O2/c1-6(2)4-5-9-7(3)8/h6H,4-5H2,1-3H3” (details)

CAS : e.g. “123-92-2” (details)

CID : e.g. “31276” (details)

SMILES : e.g. “C(C(C)C)COC(=O)C” (details)

See ?importNewData for more details. We can e.g. import data also based on CAS or CID instead of InChIKey.

#### Looking up InChIKeys

If you do not know the InChIKeys of the odorants in your data set, we recommend using the webchem package for automated lookup or doing it manually via http://cactus.nci.nih.gov/chemical/structure or any other chemical lookup service.

## Building the complete data base with CreateDatabase()

Once we imported new data we can use CreateDatabase() in order to rebuild both response matrices. During the merge process some data sets might be excluded because either their overlap with other studies is too low or the fit against other studies is too bad; these studies will be recorded in excluded.data.

## Updating parts of the data base with updateDatabase()

If we imported new data only for a few receptors, we can update the data base with updateDatabase(). There are two ways to update the data base:

### Using the heuristic approach

This is the faster way to perform a merge of all data sets. All possible binary combinations of data sets will be merged using 10 different fitting functions on the odorants that were measured in both data sets. The two data sets yielding the “best merge” (i.e. lowest mean deviations of points from the fitted function) will be merged. The process of pairwise merges will be repeated with the “merged_data” against the remaining data sets until all of them are included:

updateDatabase("Or92a", permutation = F, plot = T)
## response.matrix_non.normalized has been updated for Or92a
## response.matrix has been updated for Or92a
## excluded.data has been updated for Or92a

### Trying all permutations

The more exhaustive way to update the data base is to test all possible sequences of data set merges, calculating the mean deviations from all original data sets and selecting the merge that produces the lowest mean deviations. This approach works well for responding units that contain a low number of recorded data sets. For responding units containing 5 data sets we have to calculate merges for 120 different sequences. With 6 it is already 720 sequences and with 10 data sets we have to test > 3.6 million different sequences.

While this can be done via parallel computing, this is nothing you should try on your home PC. For the pre-computed response matrices we performed matches using the permutation approach for all responding units that contained a maximum of 10 different data sets on a computing cluster. For DoOR 2.0 these are all responding units except Or22a.

updateDatabase("Or67a", permutation = T, plot = F)
## All possible permutations (6) have been calculated, now merging.
## [1/6] Hallem.2006.EN, Gabler.2013.AL, Hallem.2004.EN ------ Mean distance: 0.0593
## [2/6] Hallem.2006.EN, Hallem.2004.EN, Gabler.2013.AL ------ Mean distance: 0.1826
## [3/6] Gabler.2013.AL, Hallem.2006.EN, Hallem.2004.EN ------ Mean distance: 0.0593
## [4/6] Gabler.2013.AL, Hallem.2004.EN, Hallem.2006.EN ------ Mean distance: 0.0597
## [5/6] Hallem.2004.EN, Hallem.2006.EN, Gabler.2013.AL ------ Mean distance: 0.0412
## [6/6] Hallem.2004.EN, Gabler.2013.AL, Hallem.2006.EN ------ Mean distance: 0.0597
## --------------------------------------------------------
## The optimized sequence with the lowest mean MD 0.0412 is:
## Hallem.2004.EN -> Hallem.2006.EN -> Gabler.2013.AL
## response.matrix_non.normalized has been updated for Or67a
## response.matrix has been updated for Or67a
## excluded.data has been updated for Or67a

## modelRP() and modelRPSEQ()

updateDatabase() and createDatabse() call modelRP() and modelRPSEQ() to perform the merges and update the different DoOR objects. If we only want to perform a merge we can call them both directly.

### Merging using the heuristic with modelRP()

modelRP() returns a list containing the merged data, the names of the excluded data sets (if any) and the names of the included data sets (if any were excluded).

merge <- modelRP(Or67a, plot = F)
knitr::kable(head(merge\$model.response))
Class Name InChIKey CID CAS merged_data
NA sfr SFR SFR SFR 0.0429749
other water XLYOFNOQVPJJNP-UHFFFAOYSA-N 962 7732-18-5 NA
amine ammonium hydroxide VHUUQVKOLVNVRT-UHFFFAOYSA-N 14923 1336-21-6 0.0788173
amine putrescine KIDHWZJUCRJVML-UHFFFAOYSA-N 1045 110-60-1 0.0313363
amine cadaverine VHRGRCVQAFMJIZ-UHFFFAOYSA-N 273 462-94-2 0.0231660
amine ammonia QGZKDVFQNNGYKY-UHFFFAOYSA-N 222 7664-41-7 NA

### Merging in a specific sequence with modelRPSEQ()

updateDatabase() with permutation = TRUE calls modelRPSEQ(). Like modelRP() we can also call modelRPSEQ directly:

SEQ <- c("Hallem.2006.EN","Kreher.2008.EN","Hallem.2006.EN")
merge <- modelRPSEQ(Or35a, SEQ = SEQ, plot = TRUE)
head(merge)
## [1] 0.09675994         NA 0.09047548 0.07062655 0.12658721         NA

## Removing a study with removeStudy()

removeStudy() will remove a data set from all DoOR data objects. If we import a data set that already exists with importNewData(), removeStudy() will automatically run before the data is imported.

removeStudy(study = "Hallem.2004.EN")
## removed Hallem.2004.EN from Or2a .
## removed Hallem.2004.EN from Or7a .
## removed Hallem.2004.EN from Or9a .
## removed Hallem.2004.EN from Or10a .
## removed Hallem.2004.EN from Or19a .
## removed Hallem.2004.EN from Or22a .
## removed Hallem.2004.EN from Or23a .
## removed Hallem.2004.EN from Or33b .
## removed Hallem.2004.EN from Or35a .
## removed Hallem.2004.EN from Or43a .
## removed Hallem.2004.EN from Or43b .
## removed Hallem.2004.EN from Or47a .
## removed Hallem.2004.EN from Or47b .
## removed Hallem.2004.EN from Or49b .
## removed Hallem.2004.EN from Or59b .
## removed Hallem.2004.EN from Or65a .
## removed Hallem.2004.EN from Or67a .
## removed Hallem.2004.EN from Or67c .
## removed Hallem.2004.EN from Or82a .
## removed Hallem.2004.EN from Or85a .
## removed Hallem.2004.EN from Or85b .
## removed Hallem.2004.EN from Or85f .
## removed Hallem.2004.EN from Or88a .
## removed Hallem.2004.EN from Or98a .
## removed Hallem.2004.EN from 'response.range'
## removed Hallem.2004.EN from 'weight.globNorm'

## Updating the odor information with updateOdorInfo()

If we edit the general odor information in DoOR.data::odor we need to update all other DoOR objects with the new information. updateOdorInfo() overwrites the first 5 columns of the DoOR responding units data frames (e.g. Or22a), it does not add or remove lines!

# Helper functions

There are several small helper functions that belong to DoOR.functions.

## transID()

Maybe the most important little function in DoOR. With transID() we can translate odorant identifiers, e.g. from CAS numbers to InChIKeys or to names. The information is taken from DoOR.data::odor, any colnames(odor) can be used to define input or output:

transID("123-92-2")
## [1] "MLFHJEHSLIIPHL-UHFFFAOYSA-N"
transID("123-92-2", to = "Name")
## [1] "isopentyl acetate"
transID("carbon dioxide", from = "Name", to = "SMILES")
## [1] "O=C=O"
odorants <- c("carbon dioxide", "pentanoic acid", "water", "benzaldehyde", "isopentyl acetate")
transID(odorants, from = "Name", to = "InChI")
## [1] "InChI=1S/CO2/c2-1-3"
## [2] "InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)"
## [3] "InChI=1S/H2O/h1H2"
## [4] "InChI=1S/C7H6O/c8-6-7-4-2-1-3-5-7/h1-6H"
## [5] "InChI=1S/C7H14O2/c1-6(2)4-5-9-7(3)8/h6H,4-5H2,1-3H3"

## resetSFR()

resetSFR() subtracts the values of a specified odorant from a response vector or from the whole response matrix. It is usually used to subtract the spontaneous firing rate of an odorant, thus setting it to zero and restoring inhibitory responses. We treat SFR like a normal odorant during the merging process, thus it becomes > 0 if negative values exist (as all data gets rescaled [0,1] before merging).

resetSFR() works either on the whole response.matrix, then an odorant InChIKey has to be specified for subtraction. Or it subtracts a value from a response vector.

rm_sfrReset <- resetSFR(x = response.matrix, sfr = "SFR")
knitr::kable(rm_sfrReset[1:10,6:15], digits = 2)
ac3B ac4 Or1a Or2a Or7a Or9a Or10a Or13a Or19a Or22a
SFR 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.02 0.01 0.02 NA 0.07 0.00 0.01 0.12 NA 0.28
VHUUQVKOLVNVRT-UHFFFAOYSA-N 0.33 0.06 NA 0.01 0.04 0.04 0.00 0.04 0.00 0.10
KIDHWZJUCRJVML-UHFFFAOYSA-N 0.37 0.00 NA 0.02 0.03 0.03 0.01 0.07 -0.02 0.09
VHRGRCVQAFMJIZ-UHFFFAOYSA-N 0.02 -0.01 NA 0.00 -0.01 0.08 -0.01 NA -0.01 0.01
QGZKDVFQNNGYKY-UHFFFAOYSA-N 0.06 0.08 NA NA 0.06 NA 0.05 0.04 NA 0.00
HZAXFHJVJLSVMW-UHFFFAOYSA-N NA 0.01 NA NA 0.06 NA 0.02 0.05 NA 0.20
WJYIASZWHGOTOU-UHFFFAOYSA-N 0.41 0.00 NA NA NA NA NA NA -0.06 NA
BMFVGAAISNGQNM-UHFFFAOYSA-N 0.32 -0.01 NA NA NA NA NA NA NA NA
ROSDSFDQCJNGOL-UHFFFAOYSA-N 0.19 0.09 NA NA NA NA NA NA NA NA
resetSFR(x = c(1:10), sfr = 4)
##  [1] -3 -2 -1  0  1  2  3  4  5  6

## default.val()

default.val() returns default values for several parameters used by the DoOR functions, e.g. the default odor identifier of the colors used in plots.

default.val("ident")
## [1] "InChIKey"
default.val("colors")
## [1] "#0570b0" "#74a9cf" "#ffffff" "#fdcc8a" "#fc8d59" "#d7301f"

## getResponses()

getResponses() returns the response values of one or several odorants across individual data sets.

odorants  <- transID(c("carbon dioxide", "isopentyl acetate"), from = "Name")
responses <- getResponses(odorants)
responses <- na.omit(responses)
knitr::kable(head(responses))
ORs studies Odor Response
25 ac3B Marshall.2010.WT CURLTUGMZLYLDI-UHFFFAOYSA-N 13
29 ac4 Marshall.2010.WT CURLTUGMZLYLDI-UHFFFAOYSA-N -1
30 ac4 Yao.2005.WT MLFHJEHSLIIPHL-UHFFFAOYSA-N 1
33 Or1a Kreher.2008.EN CURLTUGMZLYLDI-UHFFFAOYSA-N 4
34 Or1a Kreher.2008.EN MLFHJEHSLIIPHL-UHFFFAOYSA-N 21
36 Or2a Kreher.2008.EN MLFHJEHSLIIPHL-UHFFFAOYSA-N 73

## getNormalizedResponses()

getNormalizedResponses() gathers responses to the specified odorants from the response.matrix and resets the SFR via resetSFR():

odorants  <- transID(c("carbon dioxide", "isopentyl acetate"), from = "Name")
responses <- getNormalizedResponses(odorants)
responses <- na.omit(responses)
knitr::kable(head(responses))
ORs Odor Response
11 ac3B CURLTUGMZLYLDI-UHFFFAOYSA-N -0.043
13 ac4 CURLTUGMZLYLDI-UHFFFAOYSA-N -0.001
14 ac4 MLFHJEHSLIIPHL-UHFFFAOYSA-N 0.008
15 Or1a CURLTUGMZLYLDI-UHFFFAOYSA-N 0.007
16 Or1a MLFHJEHSLIIPHL-UHFFFAOYSA-N 0.068
17 Or2a CURLTUGMZLYLDI-UHFFFAOYSA-N -0.046

## countStudies()

countStudies() counts the number of studies that measured a given odorant-responding unit combination.

counts <- countStudies()
knitr::kable(counts[1:10,6:15])
ac3B ac4 Or1a Or2a Or7a Or9a Or10a Or13a Or19a Or22a
SFR 3 3 1 3 9 2 6 7 3 9
XLYOFNOQVPJJNP-UHFFFAOYSA-N 2 2 1 1 2 1 1 2 0 1
VHUUQVKOLVNVRT-UHFFFAOYSA-N 2 2 0 1 2 2 2 1 2 2
KIDHWZJUCRJVML-UHFFFAOYSA-N 3 3 0 1 4 2 3 2 2 3
VHRGRCVQAFMJIZ-UHFFFAOYSA-N 1 1 0 1 2 1 1 0 2 1
QGZKDVFQNNGYKY-UHFFFAOYSA-N 1 1 0 0 2 0 1 1 0 1
HZAXFHJVJLSVMW-UHFFFAOYSA-N 0 1 0 0 1 0 1 1 0 1
WJYIASZWHGOTOU-UHFFFAOYSA-N 1 2 0 0 0 0 0 0 1 0
BMFVGAAISNGQNM-UHFFFAOYSA-N 1 2 0 0 0 0 0 0 0 0
ROSDSFDQCJNGOL-UHFFFAOYSA-N 2 2 0 0 0 0 0 0 0 0

## exportData()

exportData() exports all or selected DoOR data objects in txt or csv format.

# exportData(".csv")                    # export all data as .csv files
# exportData(".txt", all.data = FALSE)  # export odorant responses data only as .txt files