You can install tgutil with:
remotes::install_github("tanaylab/tgutil")fread_rownames(..., row.var = "rowname")Use fread() to read a csv/tsv with row names (e.g. one created with
read.table()). The name of the column that will hold the row names is
given in row.var.
All arguments are passed to the underlying fread() call. Note that the
following arguments can’t be used (and will be silently ignored):
header, skip, col.names.
fwrite_mm(x, fname, sep = " ", row.names = TRUE, col.names = TRUE)Write the contents of the sparse matrix x into the text file fname
in the MatrixMarket format (see
http://math.nist.gov/MatrixMarket/formats.html).
The MatrixMarket format does not save row and column names.
fwrite_mm() allows saving them into separate files using the
row.names and col.names arguments. These arguments may contain file
names into which the column and row names will be written. Alternately
setting these arguments to TRUE will cause the row and column names to
be written to <fname>.rownames and <fname>.colnames respectively.
The argument sep indicates the field separator that will be used. Note
that using any field separator other than space will result in an output
that is not compliant with the MatrixMarket format.
fread_mm(fname, sep = " ", row.names = TRUE, col.names = TRUE)Reads a sparse matrix in the MatrixMarket format from the file fname.
The MatrixMarket format does not save row and column names. fread_mm()
allows reading them from separate files using the row.names and
col.names arguments. These arguments may contain file names from which
the column and row names will be read. Alternately setting these
arguments to TRUE will cause the row and column names to be read from
<fname>.rownames and <fname>.colnames respectively.