Microbial Informatics

Lecture 22

Patrick D. Schloss, PhD (microbialinformatics.github.io)
Department of Microbiology & Immunology

Announcements

  • A new homework has been posted and is due on November 22nd
    • work with a partner
    • no more than one explicit loop
  • Will have lab period on Friday
  • Read Chapters 11 in TAoRP for background material on what is discussed today

Review

  • String manipulation
  • Understand how to work with and manipulate character variables
  • What do the following do?
rev("abcdef")
paste(rev(unlist(strsplit("abcdef", ""))), collapse="")

Learning objectives

  • Finish discussing how to format output

Formatting text output with sprintf

i <- 8
sprintf("the square of %d is %d", i, i^2)

## [1] "the square of 8 is 64"

sprintf("the square root of %d is %6.2f", i, sqrt(i))

## [1] "the square root of 8 is   2.83"

sprintf("%d times 1e6 is %.3e", i, i * 1e6)

## [1] "8 times 1e6 is 8.000e+06"

Things to notice

  • %s reserves the place for an string
  • %d reserves the place for an integer
  • %f reserves the place for an decimal number
  • %e reserves the place for an number in scientific notation
  • For %f and %e the format is %m.n. n indicates the number of values to the right of the decimal place to include and m indicates the total number of spaces to allot the string
  • The output is a string
  • Of course, you can do all of this in the text block of a knitr document

Another useful way to format output to text

format(x, trim = FALSE, digits = NULL, nsmall = 0L,
       justify = c("left", "right", "centre", "none"),
       width = NULL, na.encode = TRUE, scientific = NA,
       big.mark = "",   big.interval = 3L,
       small.mark = "", small.interval = 5L,
       decimal.mark = ".", zero.print = NULL,
       drop0trailing = FALSE, ...)`
  • x is a number
  • trim is whether to right justify numbers to a common width
  • digits is the maximum number of significant digits
  • nsmall is the minimum number of digits to the right of the decimal

Special vectors

letters[1:5]

## [1] "a" "b" "c" "d" "e"

LETTERS[1:5]

## [1] "A" "B" "C" "D" "E"

Special functions to manipulate character vectors

toupper(letters[1:5])

## [1] "A" "B" "C" "D" "E"

tolower(LETTERS[1:5])

## [1] "a" "b" "c" "d" "e"

Searching for sub-strings

  • grep(pattern, x) - "Get Regular ExPression"
grep("A", c("ATA", "CCC", "CTA"))

## [1] 1 3

grep("G", c("ATA", "CCC", "CTA"))

## integer(0)
  • grep tells you which elements of x have the pattern

Searching for sub-strings

  • grepl(pattern, x) - "Get Regular ExPression" logic-based
grep("A", c("ATA", "CCC", "CTA"))

## [1] 1 3

grep("G", c("ATA", "CCC", "CTA"))

## integer(0)
  • grepl tells you whether or not each element of x ahs the pattern

Where in the string does the pattern match?

  • regexpr(pattern, x) - identify the starting position of the pattern in x
regexpr("ATG", "CTATGCATGC")

## [1] 3
## attr(,"match.length")
## [1] 3
## attr(,"useBytes")
## [1] TRUE

But what if the pattern appears multiple times?

  • gregexpr(pattern, x) - identify the starting position of the pattern throughout x ~ global
gregexpr("ATG", "CTATGCATGC")

## [[1]]
## [1] 3 7
## attr(,"match.length")
## [1] 3 3
## attr(,"useBytes")
## [1] TRUE

Find and replace

  • sub(pattern, replacement, x) - SUBstitute the PATTERN with the REPLACEMENT
sub("T", "U", "CTATGCATGC")

## [1] "CUATGCATGC"
  • Notice anything odd? What command do you think would fix this?

A global find and replace

  • gsub(pattern, replacement, x) - replaces all instances
gsub("T", "U", "CTATGCATGC")

## [1] "CUAUGCAUGC"

How would you get the complement of a DNA sequence using gsub?

dna <- "CTATGCATGC"

The complement should be GATACGTACG

A specialized find and replace

  • chartr(findChars, replaceChars, x)
chartr("T", "A", "CTATGCATGC")

## [1] "CAAAGCAAGC"

chartr("TA", "AT", "CTATGCATGC")

## [1] "CATAGCTAGC"

chartr("TACG", "ATGC", "CTATGCATGC")

## [1] "GATACGTACG"

Getting a bit more sophisticated

  • Ignoring the case of the text
grep("g", "ATGCATGC")

## integer(0)

grep("g", "ATGCATGC", ignore.case=T)

## [1] 1

Getting a bit more sophisticated

  • Location
    • ^ - Beginning of a string
    • $ - End of a string
grep("^ATG", vectorOfGenes)
grep("TAA$", vectorOfGenes)

Combining searches

  • | - Matches with either the expression before or after the pipe
grep("TAA$|TAG$", vectorOfGenes)

Let's revisit the metadata file

metadata <- read.table(file="wild.metadata.txt", header=T)
head(metadata)

##     Group Date ET Station  SP Sex Age Repro Weight Ear
## 1  5_25m3 5_25  3    BB18  PL   M   J   ABD    7.5  13
## 2  5_25m4 5_25  4     K19  PL   M   A   SCR   16.0  15
## 3  5_26m1 5_26  1     A12  PL   F   A    NE   19.5  14
## 4  5_26m9 5_26  9      M9  PL   F   A    NE   25.0  13
## 5 5_31m11 5_31 11      F2 PMG   F   J    NT   16.0  18
## 6  5_31m2 5_31  2     CC4  PL   M  SA   ABD   15.0  14
  • The Date column is the date that the mice were captured in M_DD format. Can you convert this column into "Month Day, Year" format? Assume the year was 2011.

Questions?