Summary

Samenvatting van alle hoorcolleges, werkcolleges en zelfstudies van bio-informatica (BMW11219)

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Course
Bio-informatica (BMW11219)

Institution
Universiteit Utrecht (UU)

Deze gedetailleerde samenvatting behandelt alles wat aan bod is gekomen tijdens de hoorcolleges, werkcolleges en zelfstudies van de cursus Bio-informatica aan de Universiteit Utrecht (BMW11219). Hierdoor bevat het alle informatie die nodig is voor het eindtentamen.

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Uploaded on March 9, 2023
Number of pages 214
Written in 2019/2020
Type Summary

logische operatoren
vectoren
matrices
lijsten
dataframes
factors
data importeren
kwaliteitscontrole
red flags
visualisatie
histogram
boxplot
correlatieplot
heatmap
afg
spreidingsdiagram scatter plot

Institution
Universiteit Utrecht (UU)
Education
Biomedische Wetenschappen
Course
Bio-informatica (BMW11219)

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Samenvatting
Bio-informatica
WEEK 1 T/M WEEK 10
Biomedische Wetenschappen - 2019/2020
Door Nicole (studente BMW)

,Inhoudsopgave
Bio-informatica ........................................................................................................................................ 8
Terminologie ....................................................................................................................................... 8
Databases ........................................................................................................................................ 8
Omics ............................................................................................................................................... 8
Programmeren ................................................................................................................................ 8
Toepassingen ....................................................................................................................................... 8
Sequentie analyse............................................................................................................................ 9
Eiwitstructuren .............................................................................................................................. 10
Genexpressie ................................................................................................................................. 10
Biologische netwerken .................................................................................................................. 10
Introductie R Basis ................................................................................................................................. 11
Inleiding ............................................................................................................................................. 11
Programmeren .................................................................................................................................. 11
R en RStudio .................................................................................................................................. 12
Berekeningen................................................................................................................................. 12
Datatypes .......................................................................................................................................... 14
Logische operatoren ...................................................................................................................... 14
Datastructuren .................................................................................................................................. 15
Vectoren met willekeurige waarden en karakter.......................................................................... 16
Matrices ......................................................................................................................................... 16
Lijsten en dataframes .................................................................................................................... 17
Factors ........................................................................................................................................... 18
Introductie R Importeren ...................................................................................................................... 19
Data importeren ................................................................................................................................ 19
Kwaliteitscontrole.......................................................................................................................... 22
Data selecteren ................................................................................................................................. 23
Veelvoorkomende fouten ............................................................................................................. 23
Logische operatoren ...................................................................................................................... 24
Dataframe...................................................................................................................................... 24
Data sorteren en ordenen ................................................................................................................. 25
Missende gegevens ........................................................................................................................... 26
Rode vlaggen ................................................................................................................................. 26

1

,Introductie R Grafieken ......................................................................................................................... 28
Visualisatie......................................................................................................................................... 28
Spreidingsdiagram (scatterplot) .................................................................................................... 30
Histogram ...................................................................................................................................... 31
Boxplot .......................................................................................................................................... 32
Correlatieplot ................................................................................................................................ 33
Heatmap ........................................................................................................................................ 34
Aanpassen van visualisaties .............................................................................................................. 34
Assen ............................................................................................................................................. 34
Titel ................................................................................................................................................ 34
Markers ......................................................................................................................................... 34
Legenda ......................................................................................................................................... 36
Valkuilen en leugens van visualisaties............................................................................................... 36
Afgekapte as .................................................................................................................................. 36
Dubbele as ..................................................................................................................................... 37
Selectieve contrasten (heatmaps) ................................................................................................. 37
Opslaan van plots .............................................................................................................................. 39
Introductie R Cancer genomics ............................................................................................................. 40
Sequencing ........................................................................................................................................ 41
Mutaties ........................................................................................................................................ 41
Panorama van driver mutaties ...................................................................................................... 43
TGCA dataset ..................................................................................................................................... 44
Introductie R Functies ........................................................................................................................... 45
Functies in RStudio ............................................................................................................................ 45
Scope ................................................................................................................................................. 46
If/else statements ............................................................................................................................. 47
Apply .................................................................................................................................................. 48
Varianten van apply....................................................................................................................... 49
Onderzoeksvragen en designs ............................................................................................................... 51
Onderzoekscyclus .............................................................................................................................. 51
Onderzoeksvraag ........................................................................................................................... 51
Werkplan ....................................................................................................................................... 53
Onderzoeksopzet (design) ............................................................................................................. 54

2

, Beschrijvende statistiek......................................................................................................................... 61
Statistiek in onderzoek ...................................................................................................................... 61
Kengetallen continue uitkomstmaten ............................................................................................... 62
Locatiematen ................................................................................................................................. 62
Spreidingsmaten............................................................................................................................ 64
Overzicht ....................................................................................................................................... 64
Correlatie (samenhang) ..................................................................................................................... 65
Beschrijvende statistiek in RStudio ................................................................................................... 67
Frequentiematen en associatiematen .................................................................................................. 69
Frequentiematen............................................................................................................................... 69
Prevalentie..................................................................................................................................... 69
Incidentie ....................................................................................................................................... 69
Associatiematen ................................................................................................................................ 71
Relatief risico ................................................................................................................................. 71
Risicoverschil ................................................................................................................................. 73
Odds ratio ...................................................................................................................................... 73
Datacyclus.............................................................................................................................................. 75
Inleiding ............................................................................................................................................. 75
Datamanager ................................................................................................................................. 75
UPOD ............................................................................................................................................. 75
Stap 0 ............................................................................................................................................. 75
Data verzamelen (stap 1) .................................................................................................................. 76
Data verwerken (stap 2) .................................................................................................................... 77
Data analyseren (stap 3).................................................................................................................... 78
Data publiceren (stap 4) .................................................................................................................... 79
Data archiveren (stap 5) .................................................................................................................... 80
Data hergebruiken (stap 6)................................................................................................................ 81
FAIR data ........................................................................................................................................... 82
Findable ......................................................................................................................................... 82
Accesible ........................................................................................................................................ 82
Interoperable................................................................................................................................. 82
Reusable ........................................................................................................................................ 82
Next Generation Sequencing ................................................................................................................ 83
Sanger sequencing............................................................................................................................. 83
Sequentie technologieën .................................................................................................................. 84
Library preparation............................................................................................................................ 84

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Samenvatting van alle hoorcolleges, werkcolleges en zelfstudies van bio-informatica (BMW11219)

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