parallelpam (version 1.4.3)

FilterJMatByName: FilterJMatByName

Description

Takes a jmatrix binary file containing a table with rows and columns and filters it by name, eliminating the rows or columns whose whose names are not in certain list

Usage

FilterJMatByName(fname, Gn, filname, namesat = "rows")

Value

No return value, called for side effects (creates a file)

Arguments

fname

A string with the file name of the original table

Gn

A list of R strings with the names of the rows or columns that must remain. All others will be filtered out

filname

A string with the file name of the filtered table

namesat

The string "rows" or "cols" indicating if the searched names are in the rows or in the columns of the original table. Default: "rows"

Details

If the table has no list of names in the requested dimension (rows or colums), an error is rised.
The row or column names whose names are not found obviosuly cannot remain, and the program rises a warning indicating for which row/column names this happens.
The matrix contained in the filtered file will have the same nature (full or sparse) and the same data type as the original.
This function can be used to filter either by row or by column name, with appropriate usage of parameter namesat

Examples

Rf <- matrix(runif(48),nrow=6)
rownames(Rf) <- c("A","B","C","D","E","F")
colnames(Rf) <- c("a","b","c","d","e","f","g","h")
tmpfile1=paste0(tempdir(),"/Rfullfloat.bin")
tmpfile2=paste0(tempdir(),"/Rfullfloatrowfilt.bin")
tmpfile3=paste0(tempdir(),"/Rfullfloatrowcolfilt.bin")
tmpcsvfile1=paste0(tempdir(),"/Rfullfloat.csv")
tmpcsvfile3=paste0(tempdir(),"/Rfullfloatrowcolfilt.csv")
JWriteBin(Rf,tmpfile1,dtype="float",dmtype="full",comment="Full matrix of floats")
# Let's keep only rows A, C and E
FilterJMatByName(tmpfile1,c("A","C","E"),tmpfile2,namesat="rows")
# and from the result, let's keep only columns b, d and g
FilterJMatByName(tmpfile2,c("b","d","g"),tmpfile3,namesat="cols")
JMatToCsv(tmpfile1,tmpcsvfile1)
JMatToCsv(tmpfile3,tmpcsvfile3)
# You can now compare both ASCII/csv files