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bit_R_workshop/handout.md

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welcome first day about interface second day third day looking at data loading data Exploratory analysis and visualization DEGs
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welcome

  • introduction (previous coding experiment, goal)

  • schedule

    • first day: the basics, (boring but essential)
    • second day: visualization
    • third day: follow on an online tutorial

  • posit

  • r & rstudio

first day

about interface

  • different panels
  • scripts: run, save, open
  • setting working directory
  • console
  • notebook

?sqrt

"=" versus "<-"

?sample

data <- rnorm(1000)
quantiles <- quantile(data, probs = c(0, 0.25, 0.5, 0.75, 1))
quantiles

hopefully, lunch break before Basic table functions

second day

skip the part of own function of volcano plot

third day

looking at data

airway
assays(airway)
rowData(airway)
colData(airway) #sample_table.csv
talking about the data structure

loading data

read.csv( file.path(indir, "SraRunInfo_SRP033351.csv"))

bamfiles:

library('Rsamtools')
#scanBam() will only read yieldSize number of alignments
scanBam(BamFile(filenames[1],yieldSize = 200))

Exploratory analysis and visualization

spend time on reading why transformation is needed and what are the challenges

DEGs

spend time on reading the normalization method

res@elementMetadata@listData$description
mcols(res, use.names = TRUE)
res[order(res$padj),]