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01.Preparing data for R.md

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To work with R, the data has to be in tabular format. If using Excel, mind the following points:

  • use only the necessary columns and rows in your table
  • avoid spaces in your row and column names
  • use international format for numbers (decimal symbol is a dot, not a comma!)
  • save your table as comma-delimited .csv or tab-delimited .txt

After saving, it is recommended to look at your table with a text editor. Depending on your method in R tables can be organized in different ways (here, tab-delimited):

Type I.

sample  value1  value2  value3  value4
wild.type 71  74  80  89
mutant1   0   1   0   0.5
mutant2   14  20  22  19

Type II.

wild.type  mutant1  mutant2
71   0   14
74   1   20
80   0   22
89   0.5 19

Type III. Used for various statistical methods

sample     value
wild.type  71
wild.type  74
wild.type  80
wild.type  89
mutant1    0
mutant1    1
mutant1    0
mutant1    0.5
mutant2    14
mutant2    20
mutant2    22
mutant2    19

This made-up dataset contains three samples (here, genotypes), with four values each. Type I is the usual way the table should look like, and R has methods to transform tables according to specific needs.

Note | If instead of commas, there are semicolons, use "Replace all" in Notepad and replace ; with , in the prompt. Now we are ready for working with R.