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I have two csv file - one is a list of strings and other has both strings and floating values. If the strings in both the files match I need to copy the complete row from the second file to a temporary array. I have declared a matrix with n rows and m columns and saved is as dataframe temp <- as.data.frame(matrix(nrow = n, ncol = m)). I am using for loop to iterate over all rows and strcmp to compare the strings. But when the data is written to temp the strings are stored as integers. How should I declare this array? Is it possible to write this loop without declaring an array in R?

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  • $\begingroup$ This question is unrelated to bioinformatics. You should ask somewhere more appropriate (e.g. stackoverflow). You might also want to add a minimal working example, it will be easier for other people to help you (see: stackoverflow.com/help/mcve). Good luck ! $\endgroup$ – cmdoret Apr 30 '18 at 17:39
  • $\begingroup$ I'm downvoting because this isn't really a bioinformatics question, but I suggest you take a look at dplyr::semi_join $\endgroup$ – heathobrien Apr 30 '18 at 18:57
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The merge function of R might be useful. The function expects two data frames, with [optionally] columns to compare, and it will output all fields from both data frames where the comparison columns match.

> a <- data.frame(test=1:10);
> b <- data.frame(test=c(sample(1:10,5),sample(c("A","B","C","D","E"))),
                  output=rnorm(10));
> merge(a, b, by="test");
  test     output
1    1 -1.3800443
2    2  0.2934274
3    3  0.0868700
4    9  1.1766914
5   10  0.3793448

The merge function can be customised quite a bit (e.g. if you want NA set for non-matching rows), see ?merge for more details.

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When you read in your two CSV files, you can explicitly declare the variable types for each column:

> a <- read.csv(..., colClasses=c("character"), ...)
> b <- read.csv(..., colClasses=c("character", "numeric", "numeric", ...), ...)

You could also investigate as.is or stringsAsFactors, although this can cause problems where there are duplicate strings. Using colClasses is more explicit.

Read the help documentation in ?read.csv for a more complete explanation of these operators.

You can filter with the %in% operator in match:

> strings_of_interest <- as.vector(a$V1)
> b.filtered <- b[b$V1 %in% strings_of_interest,]

If I am reading your question correctly, perhaps you can then take b.filtered and turn that into the matrix you want.

Avoid use of for loops where you can. They can slow R down considerably. A good read on this subject is in the third chapter of Patrick Burns' The R Inferno.

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  • $\begingroup$ Is there a reason for the downvoting? $\endgroup$ – Alex Reynolds Jan 9 at 18:31
  • $\begingroup$ I think it is bad for a community when downvoting without any explanation. Please explain yourself. $\endgroup$ – Alex Reynolds Jan 11 at 2:41

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