Commit 5a1a1d49 authored by Bernd Klaus's avatar Bernd Klaus

included refs, did spell checking, version used for predo 17

parent 66de9b3a
......@@ -9,7 +9,7 @@ cache = TRUE)
## ---- echo=FALSE, cache=FALSE--------------------------------------------
print(date())
## ----required_packages_and_data, echo = TRUE, cache=FALSE----------------
## ----required_packages_and_data, echo = TRUE, cache=FALSE, message=FALSE----
library("readxl")
library("BiocStyle")
library("knitr")
......@@ -145,7 +145,7 @@ pat_tiny <- filter(pat, Height < 1.7)
select(pat_tiny, PatientId, Height, Gender)
## ----light_and_small_patients, echo = TRUE-----------------------------
filter(pat, Height < 1.5, Gender == "f")
filter(pat, Height < 1.7, Gender == "f")
## ----light_or_small_patients, echo = TRUE------------------------------
filter(pat, (Height < 1.5) | (Gender == "f"))
......
......@@ -11,10 +11,11 @@ output:
code_download: true
df_print: paged
toc_depth: 2
BiocStyle::pdf_document2:
BiocStyle::pdf_document:
toc: true
highlight: tango
toc_depth: 2
bibliography: stat_methods_bioinf.bib
---
<!--
......@@ -22,7 +23,7 @@ graphics.off();rm(list=ls());rmarkdown::render('data_handling_bioinf.Rmd',
output_format = "all");purl('data_handling_bioinf.Rmd')
rmarkdown::render('data_handling_bioinf.Rmd', output_format =
BiocStyle::pdf_document2(toc = TRUE, highlight = "tango",
BiocStyle::pdf_document(toc = TRUE, highlight = "tango",
df_print = "paged", toc_depth = 2))
-->
......@@ -46,7 +47,7 @@ print(date())
# Required packages and other preparations
```{r required_packages_and_data, echo = TRUE, cache=FALSE}
```{r required_packages_and_data, echo = TRUE, cache=FALSE, message=FALSE}
library("readxl")
library("BiocStyle")
library("knitr")
......@@ -113,14 +114,14 @@ a broad scope of tolerance before T cells circulate through the body.
This "training" of the T--cells is neccessary to prevent autoimunity. It
happens by the "promiscuous" expression of numerous tissue-specific antigens
(TRAs) in medullary thymic epithelial cells (mTECs) [Kyewski and Klein, 2006].
(TRAs) in medullary thymic epithelial cells (mTECs, @Kyewski_2006).
However, it is poorly understood how this process is regulated in
single mTECs and is coordinated at the population level. Brennecke et. al.
single mTECs and is coordinated at the population level. @Brennecke_2015
obtained scRNA--Seq data of mTECs and find evidence of numerous recurring
TRA--co--expression patterns, each present in only a subset of mTECs.
Thus, they can show that the gene expression in mTEC cells rather "mosaic"
and not entirely stochastic.
Thus, they could show that the gene expression in mTEC cells rather "mosaic"
and coordianted rather than entirely stochastic.
Before we dive more deeply into the data, we review important R basics.
......@@ -459,7 +460,7 @@ For example, we can easily get light and female patients via:
```{r light_and_small_patients, echo = TRUE}
filter(pat, Height < 1.5, Gender == "f")
filter(pat, Height < 1.7, Gender == "f")
```
We can also retrieve small OR female patients via
......@@ -1012,6 +1013,7 @@ group_by(hq_cells, batch) %>%
sessionInfo()
```
# References
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library(knitcitations)
library(bibtex)
# Kyewski and Klein, 2006
citep("10.1146/annurev.immunol.23.021704.115601")
# Brennecke et. al., 2015
citep("10.1038/ni.3246")
# Pinto et. al. 2013
citep("10.1073/pnas.1308311110")
# recount2 resource
citep("10.1038/nbt.3838")
# Löhr et. al. 2013
citep("10.1371/journal.pone.0067461")
# Brennecke et. al., 2013
citep("10.1038/nmeth.2645")
# [Lun et. al.](http://dx.doi.org/10.1186/s13059-016-0947-7)
citep("10.1186/s13059-016-0947-7")
# cf. Leek et. al. 2010
citep("10.1038/nrg2825")
# [Buettner et. al.](http://dx.doi.org/10.1038/nbt.3102)
citep("10.1038/nbt.3102")
# Buja et. al. , 2007
citep("10.1198/106186008X318440")
# Kruskal, 1964
citep("10.1007/BF02289565")
write.bibtex(file = "stat_methods_bioinf.bib")
knitcitations::cleanbib()
# van der Maaten and Hinton, 2008
write("\n", file = "stat_methods_bioinf.bib", append = TRUE)
write("@article{vanDerMaaten_2008,
author = {van der Maaten, Laurens and Hinton, Geoffrey},
interhash = {370ba8b9e1909b61880a6f47c93bcd49},
intrahash = {8b9aebb404ad4a4c6a436ea413550b30},
journal = {Journal of Machine Learning Research},
pages = {2579--2605},
title = {Visualizing Data using {t-SNE} },
url = {http://www.jmlr.org/papers/v9/vandermaaten08a.html},
volume = 9,
year = 2008
}", file = "stat_methods_bioinf.bib", append = TRUE)
write("\n", file = "stat_methods_bioinf.bib", append = TRUE)
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@Article{Brennecke_2013,
doi = {10.1038/nmeth.2645},
url = {https://doi.org/10.1038/nmeth.2645},
year = {2013},
month = {sep},
publisher = {Springer Nature},
volume = {10},
number = {11},
pages = {1093--1095},
author = {Philip Brennecke and Simon Anders and Jong Kyoung Kim and Aleksandra A Ko{\l}odziejczyk and Xiuwei Zhang and Valentina Proserpio and Bianka Baying and Vladimir Benes and Sarah A Teichmann and John C Marioni and Marcus G Heisler},
title = {Accounting for technical noise in single-cell {RNA}-seq experiments},
journal = {Nature Methods},
}
@Article{Brennecke_2015,
doi = {10.1038/ni.3246},
url = {https://doi.org/10.1038/ni.3246},
year = {2015},
month = {aug},
publisher = {Springer Nature},
volume = {16},
number = {9},
pages = {933--941},
author = {Philip Brennecke and Alejandro Reyes and Sheena Pinto and Kristin Rattay and Michelle Nguyen and Rita K{\"u}chler and Wolfgang Huber and Bruno Kyewski and Lars M Steinmetz},
title = {Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells},
journal = {Nature Immunology},
}
@Article{Buettner_2015,
doi = {10.1038/nbt.3102},
url = {https://doi.org/10.1038/nbt.3102},
year = {2015},
month = {jan},
publisher = {Springer Nature},
volume = {33},
number = {2},
pages = {155--160},
author = {Florian Buettner and Kedar N Natarajan and F Paolo Casale and Valentina Proserpio and Antonio Scialdone and Fabian J Theis and Sarah A Teichmann and John C Marioni and Oliver Stegle},
title = {Computational analysis of cell-to-cell heterogeneity in single-cell {RNA}-sequencing data reveals hidden subpopulations of cells},
journal = {Nature Biotechnology},
}
@Article{Buja_2008,
doi = {10.1198/106186008x318440},
url = {https://doi.org/10.1198/106186008x318440},
year = {2008},
month = {jun},
publisher = {Informa {UK} Limited},
volume = {17},
number = {2},
pages = {444--472},
author = {Andreas Buja and Deborah F Swayne and Michael L Littman and Nathaniel Dean and Heike Hofmann and Lisha Chen},
title = {Data Visualization With Multidimensional Scaling},
journal = {Journal of Computational and Graphical Statistics},
}
@Article{Collado_Torres_2017,
doi = {10.1038/nbt.3838},
url = {https://doi.org/10.1038/nbt.3838},
year = {2017},
month = {apr},
publisher = {Springer Nature},
volume = {35},
number = {4},
pages = {319--321},
author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E Ellis and Margaret A Taub and Kasper D Hansen and Andrew E Jaffe and Ben Langmead and Jeffrey T Leek},
title = {Reproducible {RNA}-seq analysis using recount2},
journal = {Nature Biotechnology},
}
@Article{Kruskal_1964,
doi = {10.1007/bf02289565},
url = {https://doi.org/10.1007/bf02289565},
year = {1964},
month = {mar},
publisher = {Springer Nature},
volume = {29},
number = {1},
pages = {1--27},
author = {J. B. Kruskal},
title = {Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis},
journal = {Psychometrika},
}
@Article{Kyewski_2006,
doi = {10.1146/annurev.immunol.23.021704.115601},
url = {https://doi.org/10.1146/annurev.immunol.23.021704.115601},
year = {2006},
month = {apr},
publisher = {Annual Reviews},
volume = {24},
number = {1},
pages = {571--606},
author = {Bruno Kyewski and Ludger Klein},
title = {A {CENTRAL} {ROLE} {FOR} {CENTRAL} {TOLERANCE}},
journal = {Annual Review of Immunology},
}
@Article{Leek_2010,
doi = {10.1038/nrg2825},
url = {https://doi.org/10.1038/nrg2825},
year = {2010},
month = {sep},
publisher = {Springer Nature},
volume = {11},
number = {10},
pages = {733--739},
author = {Jeffrey T. Leek and Robert B. Scharpf and H{\a'e}ctor Corrada Bravo and David Simcha and Benjamin Langmead and W. Evan Johnson and Donald Geman and Keith Baggerly and Rafael A. Irizarry},
title = {Tackling the widespread and critical impact of batch effects in high-throughput data},
journal = {Nature Reviews Genetics},
}
@Article{L_Lun_2016,
doi = {10.1186/s13059-016-0947-7},
url = {https://doi.org/10.1186/s13059-016-0947-7},
year = {2016},
month = {apr},
publisher = {Springer Nature},
volume = {17},
number = {1},
author = {Aaron T. L. Lun and Karsten Bach and John C. Marioni},
title = {Pooling across cells to normalize single-cell {RNA} sequencing data with many zero counts},
journal = {Genome Biology},
}
@Article{Pinto_2013,
doi = {10.1073/pnas.1308311110},
url = {https://doi.org/10.1073/pnas.1308311110},
year = {2013},
month = {aug},
publisher = {Proceedings of the National Academy of Sciences},
volume = {110},
number = {37},
pages = {E3497--E3505},
author = {S. Pinto and C. Michel and H. Schmidt-Glenewinkel and N. Harder and K. Rohr and S. Wild and B. Brors and B. Kyewski},
title = {Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity},
journal = {Proceedings of the National Academy of Sciences},
}
@Article{R_hr_2013,
doi = {10.1371/journal.pone.0067461},
url = {https://doi.org/10.1371/journal.pone.0067461},
year = {2013},
month = {jul},
publisher = {Public Library of Science ({PLoS})},
volume = {8},
number = {7},
pages = {e67461},
author = {Christina R{\"o}hr and Martin Kerick and Axel Fischer and Alexander K{\"u}hn and Karl Kashofer and Bernd Timmermann and Andriani Daskalaki and Thomas Meinel and Dmitriy Drichel and Stefan T. B{\"o}rno and Anja Nowka and Sylvia Krobitsch and Alice C. McHardy and Christina Kratsch and Tim Becker and Andrea Wunderlich and Christian Barmeyer and Christian Viertler and Kurt Zatloukal and Christoph Wierling and Hans Lehrach and Michal R. Schweiger},
editor = {Peter Csermely},
title = {High-Throughput {miRNA} and {mRNA} Sequencing of Paired Colorectal Normal, Tumor and Metastasis Tissues and Bioinformatic Modeling of {miRNA}-1 Therapeutic Applications},
journal = {{PLoS} {ONE}},
}
@article{vanDerMaaten_2008,
author = {van der Maaten, Laurens and Hinton, Geoffrey},
interhash = {370ba8b9e1909b61880a6f47c93bcd49},
intrahash = {8b9aebb404ad4a4c6a436ea413550b30},
journal = {Journal of Machine Learning Research},
pages = {2579--2605},
title = {Visualizing Data using {t-SNE} },
url = {http://www.jmlr.org/papers/v9/vandermaaten08a.html},
volume = 9,
year = 2008
}
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