RPR-OBJECTS-Data frames
R "data frames""
(R data frames)
Abstract:
Introduction to data frames: how to create, and modify them and how to retrieve data.
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Prerequisites:
This unit builds on material covered in the following prerequisite units:
Contents
Contents
Task:
- Load the
R-Exercise_BasicSetupproject in RStudio if you don't already have it open. - Type
init()as instructed after the project has loaded. - Continue below.
Data frames
Data frames are probably the most important type of data object for bioinformatics in R; they emulate our mental model of data in a spreadsheet and can be used to implement entity-relationship datamodels.
Usually the result of reading external data from an input file is a data frame. The file below is included with the R-Exercise-BasicSetup project files - it is called plasmidData.tsv, and you can click on it in the Files Pane to open and inspect it.
Name Size Marker Ori Sites pUC19 2686 Amp ColE1 EcoRI, SacI, SmaI, BamHI, XbaI, PstI, HindIII pBR322 4361 Amp, Tet ColE1 EcoRI, ClaI, HindIII pACYC184 4245 Tet, Cam p15A ClaI, HindIII
This data set uses tabs as column separators and it has a header line. Similar files can be exported from Excel or other spreadsheet programs. Read this as a data frame as follows:
( plasmidData <- read.table("plasmidData.tsv",
sep="\t",
header=TRUE,
stringsAsFactors = FALSE) )
objectInfo(plasmidData)Note the argument stringsAsFactors = FALSE. If this is TRUE instead, R will convert all strings in the input to factors and this may lead to problems. Make it a habit to turn this behaviour off, you can always turn a column of strings into factors when you actually mean to have factors.
You can view the data frame contents by clicking on the spreadsheet icon behind its name in the Environment Pane.
Basic operations
Here are some basic operations with the data frame. Try them and experiment. If you break it by mistake, you can just recreate it by reading the source file again:
rownames(plasmidData) <- plasmidData[ , 1] # use column 1 as rownames
nrow(plasmidData)
ncol(plasmidData)
objectInfo(plasmidData)
x <- plasmidData[2, ] # assign one row to a variable
objectInfo(x) # This is also a data frame! One row. It has to be, because
# it contains elements of type chr and of type int!
plasmidData["pBR322", ] # retrieve one row: different syntax, same thing
plasmidData[ , 2] # retrieve one column
plasmidData[ , "Size"] # retrieve one column: same principle
plasmidData <- plasmidData[-2, ] # remove one row
objectInfo(plasmidData)
plasmidData <- rbind(plasmidData, x) # add it back at the end
objectInfo(plasmidData)
# add a new row from scratch:
plasmidData <- rbind(plasmidData, data.frame(Name = "pMAL-p5x",
Size = 5752,
Marker = "Amp",
Ori = "pMB1",
Sites = "SacI, AvaI, ..., HindIII",
stringsAsFactors = FALSE))
objectInfo(plasmidData)Task:
The rowname of the new row of plasmidData is now "1". It should be "pMAL-p5x". Fix this.
Self-evaluation
Notes
Further reading, links and resources
If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2018-05-05
Version:
- 1.0.1
Version history:
- 1.0.1 Maintenance
- 1.0 Completed to first live version
- 0.1 Material collected from previous tutorial
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