vignettes/vignette.md
In microbiome/HITChipDB: HITChipDB
title: "HITChipDB vignette"
author: "Leo Lahti and Jarkko Salojarvi"
date: "2015-06-28"
output: md_document
HITChipDB R package
Installation
Install/upload and loading the release version
It is advisable to run this before every analysis to use the latest version:
install.packages("devtools")
library(devtools)
install_github("microbiome/HITChipDB")
Extracting HITChip data from the MySQL database ('profiling')
Instructions to extract data from database (HIT/MIT/PIT/ChickChip)
Oligo heatmap
To reproduce the oligo-level heatmap from the profiling script, modify this example
Read data from SQL database
Read MySQL data for specified projects (request usernames, passwords, etc. from the admins):
library(HITChipDB)
proj <- c("MetaHIT") # List projects to be extracted; see list.mysql.projects for a complete list
dbuser = "myusername"; # Request username from the admins
dbpwd = "mypasswd"; # Request password from the admins
host <- NULL; # Used with HITChip FTP server; ask details from admins
port <- NULL; # Used with HITChip FTP server; ask details from admins
# Get sample information matrix for the selected projects
project.info <- fetch.sample.info(proj, dbuser = dbuser, dbpwd = dbpwd, dbname = "Phyloarray", host = host, port = port)
List projects in MySQL database
projs <- list.mysql.projects(dbuser, dbpwd, dbname, host = NULL, port = NULL)
Retrieving microarray data
HITChip Use virtual machine or WUR database computer through FTP
connection to Helsinki database. Once you have opened the
connection, see the instructions above on how to read the data in R.
To access HITChip FTP database from your own computer, install the
virtual machine. For further instructions, contact the admins.
After installing the virtual machine, see R instructions for
HITChip.
MITChip, PITChip, ChickChip Use WUR database computer
(instructions)
Further SQL functions
- get.phylogeny.info: from the MySQL db
- fetch.projects: Fetch projects from the phyloarray MySQL database
- fetch.samples: Fetch samples from the phyloarray MySQL database
- fetch.sample.info: Fetch sample information from HITChip atlas
Licensing and Citations
This work can be freely used, modified and distributed under the
Two-clause FreeBSD license.
Kindly cite the work as 'Leo Lahti and Jarkko Salojarvi
(2014). microbiome R package. URL: http://microbiome.github.com'.
Session info
This vignette was created with
sessionInfo()
## R version 3.2.1 (2015-06-18)
## Platform: x86_64-unknown-linux-gnu (64-bit)
## Running under: Ubuntu 15.04
##
## 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] tcltk parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] HITChipDB_0.5.25 RMySQL_0.10.3 preprocessCore_1.30.0
## [4] DBI_0.3.1 microbiome_0.99.55 RPA_1.24.0
## [7] affy_1.46.1 Biobase_2.28.0 BiocGenerics_0.14.0
## [10] phyloseq_1.13.2 rmarkdown_0.7 knitr_1.10.5
## [13] scimapClient_0.2.1
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.2-6 som_0.3-5
## [3] futile.logger_1.4.1 XVector_0.8.0
## [5] OAIHarvester_0.1-7 RcppArmadillo_0.5.200.1.0
## [7] GenomicRanges_1.20.5 affyio_1.36.0
## [9] AnnotationDbi_1.30.1 codetools_0.2-11
## [11] splines_3.2.1 geneplotter_1.46.0
## [13] mixOmics_5.0-4 tgp_2.4-11
## [15] ade4_1.7-2 spam_1.0-1
## [17] Formula_1.2-1 annotate_1.46.0
## [19] cluster_2.0.2 pheatmap_1.0.2
## [21] Kendall_2.2 sorvi_0.7.26
## [23] assertthat_0.1 Matrix_1.2-1
## [25] formatR_1.2 acepack_1.3-3.3
## [27] htmltools_0.2.6 tools_3.2.1
## [29] igraph_0.7.1 rdryad_0.1.1
## [31] gtable_0.1.2 reshape2_1.4.1
## [33] dplyr_0.4.2 maps_2.3-9
## [35] Rcpp_0.11.6 Biostrings_2.36.1
## [37] RJSONIO_1.3-0 multtest_2.24.0
## [39] biom_0.3.12 gdata_2.16.1
## [41] ape_3.3 nlme_3.1-120
## [43] iterators_1.0.7 lmtest_0.9-34
## [45] stringr_1.0.0 proto_0.3-10
## [47] gtools_3.5.0 XML_3.98-1.2
## [49] zlibbioc_1.14.0 MASS_7.3-41
## [51] zoo_1.7-12 scales_0.2.5
## [53] BiocInstaller_1.18.3 lambda.r_1.1.7
## [55] RColorBrewer_1.1-2 fields_8.2-1
## [57] yaml_2.1.13 gridExtra_0.9.1
## [59] ggplot2_1.0.1 rpart_4.1-9
## [61] latticeExtra_0.6-26 stringi_0.5-2
## [63] maptree_1.4-7 RSQLite_1.0.0
## [65] genefilter_1.50.0 S4Vectors_0.6.0
## [67] tseries_0.10-34 foreach_1.4.2
## [69] nortest_1.0-3 permute_0.8-4
## [71] boot_1.3-16 BiocParallel_1.2.5
## [73] chron_2.3-46 GenomeInfoDb_1.4.1
## [75] moments_0.14 bitops_1.0-6
## [77] rgl_0.95.1247 evaluate_0.7
## [79] lattice_0.20-31 plyr_1.8.3
## [81] magrittr_1.5 DESeq2_1.8.1
## [83] R6_2.0.1 IRanges_2.2.4
## [85] earlywarnings_1.1.21 Hmisc_3.16-0
## [87] foreign_0.8-63 mgcv_1.8-6
## [89] survival_2.38-2 RCurl_1.95-4.6
## [91] nnet_7.3-9 futile.options_1.0.0
## [93] KernSmooth_2.23-14 RGCCA_2.0
## [95] locfit_1.5-9.1 grid_3.2.1
## [97] data.table_1.9.4 vegan_2.3-0
## [99] digest_0.6.8 diptest_0.75-7
## [101] xtable_1.7-4 stats4_3.2.1
## [103] munsell_0.4.2 quadprog_1.5-5
microbiome/HITChipDB documentation built on June 7, 2020, 8:25 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "HITChipDB vignette" author: "Leo Lahti and Jarkko Salojarvi" date: "2015-06-28" output: md_document
HITChipDB R package
Installation
Install/upload and loading the release version
It is advisable to run this before every analysis to use the latest version:
install.packages("devtools")
library(devtools)
install_github("microbiome/HITChipDB")
Extracting HITChip data from the MySQL database ('profiling')
Instructions to extract data from database (HIT/MIT/PIT/ChickChip)
Oligo heatmap
To reproduce the oligo-level heatmap from the profiling script, modify this example
Read data from SQL database
Read MySQL data for specified projects (request usernames, passwords, etc. from the admins):
library(HITChipDB)
proj <- c("MetaHIT") # List projects to be extracted; see list.mysql.projects for a complete list
dbuser = "myusername"; # Request username from the admins
dbpwd = "mypasswd"; # Request password from the admins
host <- NULL; # Used with HITChip FTP server; ask details from admins
port <- NULL; # Used with HITChip FTP server; ask details from admins
# Get sample information matrix for the selected projects
project.info <- fetch.sample.info(proj, dbuser = dbuser, dbpwd = dbpwd, dbname = "Phyloarray", host = host, port = port)
List projects in MySQL database
projs <- list.mysql.projects(dbuser, dbpwd, dbname, host = NULL, port = NULL)
Retrieving microarray data
HITChip Use virtual machine or WUR database computer through FTP connection to Helsinki database. Once you have opened the connection, see the instructions above on how to read the data in R.
To access HITChip FTP database from your own computer, install the virtual machine. For further instructions, contact the admins.
After installing the virtual machine, see R instructions for HITChip.
MITChip, PITChip, ChickChip Use WUR database computer (instructions)
Further SQL functions
- get.phylogeny.info: from the MySQL db
- fetch.projects: Fetch projects from the phyloarray MySQL database
- fetch.samples: Fetch samples from the phyloarray MySQL database
- fetch.sample.info: Fetch sample information from HITChip atlas
Licensing and Citations
This work can be freely used, modified and distributed under the Two-clause FreeBSD license.
Kindly cite the work as 'Leo Lahti and Jarkko Salojarvi (2014). microbiome R package. URL: http://microbiome.github.com'.
Session info
This vignette was created with
sessionInfo()
## R version 3.2.1 (2015-06-18)
## Platform: x86_64-unknown-linux-gnu (64-bit)
## Running under: Ubuntu 15.04
##
## 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] tcltk parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] HITChipDB_0.5.25 RMySQL_0.10.3 preprocessCore_1.30.0
## [4] DBI_0.3.1 microbiome_0.99.55 RPA_1.24.0
## [7] affy_1.46.1 Biobase_2.28.0 BiocGenerics_0.14.0
## [10] phyloseq_1.13.2 rmarkdown_0.7 knitr_1.10.5
## [13] scimapClient_0.2.1
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.2-6 som_0.3-5
## [3] futile.logger_1.4.1 XVector_0.8.0
## [5] OAIHarvester_0.1-7 RcppArmadillo_0.5.200.1.0
## [7] GenomicRanges_1.20.5 affyio_1.36.0
## [9] AnnotationDbi_1.30.1 codetools_0.2-11
## [11] splines_3.2.1 geneplotter_1.46.0
## [13] mixOmics_5.0-4 tgp_2.4-11
## [15] ade4_1.7-2 spam_1.0-1
## [17] Formula_1.2-1 annotate_1.46.0
## [19] cluster_2.0.2 pheatmap_1.0.2
## [21] Kendall_2.2 sorvi_0.7.26
## [23] assertthat_0.1 Matrix_1.2-1
## [25] formatR_1.2 acepack_1.3-3.3
## [27] htmltools_0.2.6 tools_3.2.1
## [29] igraph_0.7.1 rdryad_0.1.1
## [31] gtable_0.1.2 reshape2_1.4.1
## [33] dplyr_0.4.2 maps_2.3-9
## [35] Rcpp_0.11.6 Biostrings_2.36.1
## [37] RJSONIO_1.3-0 multtest_2.24.0
## [39] biom_0.3.12 gdata_2.16.1
## [41] ape_3.3 nlme_3.1-120
## [43] iterators_1.0.7 lmtest_0.9-34
## [45] stringr_1.0.0 proto_0.3-10
## [47] gtools_3.5.0 XML_3.98-1.2
## [49] zlibbioc_1.14.0 MASS_7.3-41
## [51] zoo_1.7-12 scales_0.2.5
## [53] BiocInstaller_1.18.3 lambda.r_1.1.7
## [55] RColorBrewer_1.1-2 fields_8.2-1
## [57] yaml_2.1.13 gridExtra_0.9.1
## [59] ggplot2_1.0.1 rpart_4.1-9
## [61] latticeExtra_0.6-26 stringi_0.5-2
## [63] maptree_1.4-7 RSQLite_1.0.0
## [65] genefilter_1.50.0 S4Vectors_0.6.0
## [67] tseries_0.10-34 foreach_1.4.2
## [69] nortest_1.0-3 permute_0.8-4
## [71] boot_1.3-16 BiocParallel_1.2.5
## [73] chron_2.3-46 GenomeInfoDb_1.4.1
## [75] moments_0.14 bitops_1.0-6
## [77] rgl_0.95.1247 evaluate_0.7
## [79] lattice_0.20-31 plyr_1.8.3
## [81] magrittr_1.5 DESeq2_1.8.1
## [83] R6_2.0.1 IRanges_2.2.4
## [85] earlywarnings_1.1.21 Hmisc_3.16-0
## [87] foreign_0.8-63 mgcv_1.8-6
## [89] survival_2.38-2 RCurl_1.95-4.6
## [91] nnet_7.3-9 futile.options_1.0.0
## [93] KernSmooth_2.23-14 RGCCA_2.0
## [95] locfit_1.5-9.1 grid_3.2.1
## [97] data.table_1.9.4 vegan_2.3-0
## [99] digest_0.6.8 diptest_0.75-7
## [101] xtable_1.7-4 stats4_3.2.1
## [103] munsell_0.4.2 quadprog_1.5-5
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