Class 4: GC content of all genes. Patterns and Abstraction
Computing for Molecular Biology 2
Andrés Aravena, PhD
19 March 2021
We will work with E.coli genes today
We enable the seqinr package
Then we load all genes into a named list. Verify that you are using the correct file: all protein coding genes.
Let’s verify that the number of genes is correct
[1] 4140GC content of every gene
How can we calculate GC for every gene
As usual we start by decomposing the problem into smaller parts
- we will calculate the GC content one gene each time
- our input is the list
genes
In other words, we assume that the command read.fasta() was already used and its result was stored in genes
Solution 1
V <- toupper(genes[[1]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5151515V <- toupper(genes[[2]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5306537Solution 1, page 2
V <- toupper(genes[[3]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.562701V <- toupper(genes[[4]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5283605Solution 1, page 3
V <- toupper(genes[[5]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5387205V <- toupper(genes[[6]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.4967825Solution 1, page 4
V <- toupper(genes[[7]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5331936V <- toupper(genes[[8]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)[1] 0.5199161and so on, until gene[[4140]]
We are working for the computer
Even using copy-and-paste this solution is boring
So we use the second took of computational thinking
Pattern recognition
Looking for a pattern
compare the code for the first gene…
V <- toupper(genes[[1]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)…against the code for the second gene
V <- toupper(genes[[2]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)what do these codes have in common?
Recognizing a pattern
Both codes look like this
V <- toupper(genes[[something]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)they are not 100% identical, but they are “the same”
Finding patterns is good
We decomposed the problem into smaller parts
Then we recognized a pattern on each part
Now we can use the next tool: abstraction
We will wrap all the pattern into a function
Functions
Functions in R
- How do you write a new function in R?
- What are its parts?
- How many of each part?
Functions in R
Function for gene GC content, version 1
gene_GC_content_v1 <- function(i) {
V <- toupper(genes[[i]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
print(GC_content)
}- name is
gene_GC_content_v1 - input is
i, the index of gene - no output, but printing on the screen
Using our first function
[1] 0.5151515[1] 0.5306537[1] 0.562701[1] 0.5283605[1] 0.5387205print() is not good
What if we do not want to print the numbers?
What if we want to store them in a vector?
all_GC_content <- c(gene_GC_content_v1(1),
gene_GC_content_v1(2),
gene_GC_content_v1(3),
gene_GC_content_v1(4),
gene_GC_content_v1(5))[1] 0.5151515
[1] 0.5306537
[1] 0.562701
[1] 0.5283605
[1] 0.5387205[1] 0.5151515 0.5306537 0.5627010 0.5283605 0.5387205Better: return() the results
Function for gene GC content, version 2
gene_GC_content_v2 <- function(i) {
V <- toupper(genes[[i]])
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
return(GC_content)
}- output is GC content
Using the second version
all_GC_content <- c(gene_GC_content_v2(1),
gene_GC_content_v2(2),
gene_GC_content_v2(3),
gene_GC_content_v2(4),
gene_GC_content_v2(5))
all_GC_content[1] 0.5151515 0.5306537 0.5627010 0.5283605 0.5387205This time nothing is printed, and we can decide later what to do with the result.
Calculating for all genes
We do not want to do boring work.
The computer can do it for us
How can we apply gene_GC_content_v2() to each element of the list
Vector-to-vector functions
Some functions take a vector and return a vector of the same length.
[1] 1 2 3 4 5 6[1] 0.0000000 0.6931472 1.0986123[1] 2.718282 7.389056 20.085537(we normally use them with a vector of length 1)
Vector-to-value functions
Other functions take a vector and return a single value
[1] 1[1] 15.16667[1] 12.5[1] 36Our function can take only one value
If we give it a vector, it fails
Error in genes[[i]]: recursive indexing failed at level 2Applying a function to a vector
To apply a function to each element of a vector, we can use lapply(). The result is a list
[[1]]
[1] 0.5151515
[[2]]
[1] 0.5306537
[[3]]
[1] 0.562701
[[4]]
[1] 0.5283605
[[5]]
[1] 0.5387205Application with simple output
List are great, but sometimes we want something simple, like a vector.
In that case we use sapply()
[1] 0.5151515 0.5306537 0.5627010 0.5283605 0.5387205GC of all the genome
GC content of E.coli genome
chromosomes <- read.fasta("NC_000913.fna", seqtype="DNA", set.attributes = FALSE)
length(chromosomes)[1] 1GC content of E.coli genome
V <- toupper(genome)
count_C <- sum(V=="C")
count_G <- sum(V=="G")
GC_content <- (count_C +count_G)/length(V)
GC_content[1] 0.5079071function for GC content, version 3
using it
[1] 0.5079071 lcl|NC_000913.3_cds_NP_414542.1_1
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lcl|NC_000913.3_cds_NP_418790.1_4288
0.5234899
lcl|NC_000913.3_cds_NP_418791.1_4289
0.5353982
lcl|NC_000913.3_cds_NP_418792.1_4290
0.5402516
lcl|NC_000913.3_cds_NP_418793.1_4291
0.5165017
lcl|NC_000913.3_cds_YP_588479.2_4292
0.5185185
lcl|NC_000913.3_cds_NP_418794.1_4293
0.5391061
lcl|NC_000913.3_cds_YP_026291.2_4294
0.5551282
lcl|NC_000913.3_cds_NP_418796.1_4295
0.5636574
lcl|NC_000913.3_cds_NP_418797.1_4296
0.5312701
lcl|NC_000913.3_cds_NP_418798.1_4297
0.5538462
lcl|NC_000913.3_cds_NP_418799.1_4298
0.5517763
lcl|NC_000913.3_cds_NP_418800.1_4299
0.5433007
lcl|NC_000913.3_cds_NP_418801.1_4300
0.5236111
lcl|NC_000913.3_cds_NP_418802.1_4301
0.5382883
lcl|NC_000913.3_cds_NP_418803.1_4302
0.5781711
lcl|NC_000913.3_cds_NP_418804.1_4303
0.5565891
lcl|NC_000913.3_cds_NP_418805.1_4304
0.5665635
lcl|NC_000913.3_cds_NP_418806.1_4305
0.5770065
lcl|NC_000913.3_cds_NP_418807.4_4306
0.5093268
lcl|NC_000913.3_cds_NP_418808.1_4307
0.5473621
lcl|NC_000913.3_cds_NP_418809.4_4308
0.5454076
lcl|NC_000913.3_cds_NP_418810.1_4309
0.5412844
lcl|NC_000913.3_cds_NP_418811.2_4310
0.5614035
lcl|NC_000913.3_cds_NP_418812.1_4311
0.5617284
lcl|NC_000913.3_cds_NP_418813.1_4312
0.5321839
lcl|NC_000913.3_cds_NP_418814.1_4313
0.4894515
lcl|NC_000913.3_cds_NP_418815.1_4314
0.5521739
lcl|NC_000913.3_cds_NP_418816.1_4315
0.5389474
lcl|NC_000913.3_cds_NP_418817.1_4316
0.4959350
lcl|NC_000913.3_cds_NP_418818.1_4317
0.5104603
lcl|NC_000913.3_cds_NP_418819.1_4318
0.4255319
lcl|NC_000913.3_cds_NP_418820.1_4319
0.4978166 using it
Summary
Creating our first function
To create a function we use a code like this:
- All functions need one or more inputs
- Most functions also give one output
- output is optional, but is a good idea
- We need to choose a function name.
Sometimes this may not be easy lapply()andsapply()are great. Learn them!