R framework for exploration and analysis of respirometry data

Description

This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.

Details

Index:

BuxcoDB-class           Class '"BuxcoDB"'
dbImport                Import data into a BuxcoDB database
parse.buxco             Functions for parsing Buxco respirometry data
plethy-package          R framework for exploration and analysis of
                        respirometry data
buxco.sample.data.path  Path to a sample Buxco output file
sample.db.path          Path to a sample BuxcoDB database

Further information is available in the following vignettes:

Author(s)

Daniel Bottomly, Marty Ferris

Maintainer: Daniel Bottomly <bottomly@ohsu.edu>

References

www.buxco.com

Examples

tmp_db <- tempfile()

bux.db <- parse.buxco(file.name=buxco.sample.data.path(), db.name = tmp_db)

head(retrieveData(bux.db))

bux.db <- makeBuxcoDB(tmp_db)

samples(bux.db)
variables(bux.db)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(plethy)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/plethy/plethy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plethy-package
> ### Title: R framework for exploration and analysis of respirometry data
> ### Aliases: plethy-package plethy buxco.sample.data.path sample.db.path
> ### Keywords: package
> 
> ### ** Examples
> 
> tmp_db <- tempfile()
> 
> bux.db <- parse.buxco(file.name=buxco.sample.data.path(), db.name = tmp_db)
Processing /home/ddbj/local/lib64/R/library/plethy/extdata/BuxcoR_sample.csv in chunks of 500
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample 8034x13140_5
Sample written
Processing breakpoint 2
Starting sample 8034x13140_11
Sample written
Starting sample 8034x13140_5
Sample written
Processing breakpoint 3
Starting sample 8034x13140_11
Sample written
Starting sample 8034x13140_2
Sample written
Processing breakpoint 4
Starting sample 8034x13140_2
Sample written
Starting sample 8034x13140_3
Sample written
Starting chunk 2
Reached breakpoint change
Processing breakpoint 5
Starting sample 8034x13140_1
Sample written
Starting sample 8034x13140_3
Sample written
Processing breakpoint 6
Starting sample 8034x13140_1
Sample written
Starting sample 8034x13140_9
Sample written
Processing breakpoint 7
Starting sample 8034x13140_4
Sample written
Starting sample 8034x13140_9
Sample written
Starting chunk 3
Reached breakpoint change
Processing breakpoint 8
Starting sample 8034x13140_10
Sample written
Starting sample 8034x13140_4
Sample written
Reached the end of the file, writing remaining data
Starting sample 8034x13140_10
Sample written
> 
> head(retrieveData(bux.db))
   Sample_Name              P_Time Break_sec_start Variable_Name Bux_table_Name
1 8034x13140_5 2012-09-28 10:07:17               0             f          WBPth
2 8034x13140_5 2012-09-28 10:07:17               0           TVb          WBPth
3 8034x13140_5 2012-09-28 10:07:17               0           MVb          WBPth
4 8034x13140_5 2012-09-28 10:07:17               0          Penh          WBPth
5 8034x13140_5 2012-09-28 10:07:17               0           PAU          WBPth
6 8034x13140_5 2012-09-28 10:07:17               0          Rpef          WBPth
  Rec_Exp_date Break_number       Value
1          D-3            1 384.3611755
2          D-3            1   0.1556593
3          D-3            1  59.8293839
4          D-3            1   0.5106936
5          D-3            1   1.6047863
6          D-3            1   0.0828647
> 
> bux.db <- makeBuxcoDB(tmp_db)
> 
> samples(bux.db)
[1] "8034x13140_5"  "8034x13140_11" "8034x13140_2"  "8034x13140_3" 
[5] "8034x13140_1"  "8034x13140_9"  "8034x13140_4"  "8034x13140_10"
> variables(bux.db)
 [1] "f"     "TVb"   "MVb"   "Penh"  "PAU"   "Rpef"  "Comp"  "PIFb"  "PEFb" 
[10] "Ti"    "Te"    "EF50"  "Tr"    "Tbody" "Tc"    "RH"    "Rinx" 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>