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Samenvatting van alle hoorcolleges, werkcolleges en zelfstudies van bio-informatica (BMW11219) $9.68
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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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Document information

  • March 9, 2023
  • 214
  • 2019/2020
  • Summary

Subjects

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

Written for

  • Universiteit Utrecht (UU)
  • Biomedische Wetenschappen
  • 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




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,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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