In tkonopka/shrt: short R code

This vignette demonstrates functions in the files range.

library(shrt)

It will be handy to work with a small table

d1 = mtrx(letters[1:8], col.names=LETTERS[1:4], row.names=c("R1", "R2"))
d1

 

wtht

wtht is a wrapper for write.table which by default has row.names=FALSE, col.names=TRUE, quote=FALSE, and sep='\t'. The basic usage save a table into a specified file

wtht(d1, file="test.1.tsv")

wtht also provides a way to record row names in a named column. In this mode, the function creates a temporary data structure with a new column, and save this new structure to disk.

wtht(d1, file="test.2.tsv", rowid.column="rowid")

Refer to the next section to see the result from these commands.

 

rtht

rtht is a wrapper for read.table which by default sets header=TRUE, sep='\t', and stringsAsFactors=FALSE.

We can use this function to see the files saved above. We can read the first table.

d2 = rtht("test.1.tsv")
d2

Note that row names are absent in this object - they are not recorded in the file.

The second file we created was meant to contain row names in a new column. We can verify this by reading the file with the same syntax as above

d3 = rtht("test.2.tsv")
d3

Note here that the table contains a column rowid that did not appear in the original dataset. We can optionally eliminate this column whilst reading the data.

d4 = rtht("test.2.tsv", rowid.column="rowid")
d4

This result is now almost equivalent to the orignal data. (Note d1 was a matrix, but reading a table from disk always returns a data frame.)

unlink("test.1.tsv")
unlink("test.2.tsv")

 

load1

load1 retrieves data from a file on disk in a similar way to load. However, load1 is specialized to loading single objects from a file. This is handy in situations such as demonstrated below.

Let's save our matrix into an Rda file

save(d1, file="test.Rda")

The best way to check that the data is really saved would be to load it into a new R session. Here, we can achieve a similar effect by removing the variable from the environment and then loading it from the file.

rm(d1)
d1

As expected, this returned an error. But we can now load the data from the saved file.

load("test.Rda")
d1

A 'feature' of the standard load function is that data is associated with the same object names as at the time of save. In this case, the matrix appears in the object called d1.

However, this behavior is not always desirable. If we already have an object d1 in the environment, loading from file would over-write our data.

d1 = "Important"
d1
load("test.Rda")
d1

Thus, we can loose important information through loading of external data. This is where load1 can be useful

d1 = "Important"
d1
dfile = load1("test.Rda")
d1
dfile

Thus, we keep all objects in our environment intact and assign the new data into a variable of our choice.

unlink("test.Rda")

 

tkonopka/shrt documentation built on March 5, 2020, 2:51 p.m.