- normed.data
The normalized data. A list of two matrices,
usually coming from isa.normalize
.
- row.seeds
The row seed vectors to start the ISA runs
from. Every column is a seed vector. (If this argument and
col.seeds
are both present, then both of them are used.)
- col.seeds
The column seed vectors to start the ISA runs from,
every column is a seed vector. (If this argument and
row.seeds
are both present, then both of them are used.)
- thr.row
Numeric scalar or vector giving the threshold parameter
for the rows. Higher values indicate a more stringent threshold and
the result biclusters will contain less rows on average. The
threshold is measured by the number of standard deviations from the
mean, over the values of the row vector. If it is a vector then it
must contain an entry for each seed.
- thr.col
Numeric scalar or vector giving the threshold parameter
for the columns. The analogue of thr.row
.
- direction
Character vector of length two, one for the rows, one
for the columns. It specifies whether we are interested in
rows/columns that are higher (‘up
’) than average,
lower than average (‘down
’), or both
(‘updown
’).
- convergence
Character scalar, the convergence criteria for the
ISA iteration. If it is ‘cor
’, then convergence is
measured based on high Pearson correlation (see the cor.limit
argument below) of the subsequent row and
column vectors. If it is ‘eps
’, then all entries of
the subsequent row and column vectors must be close to each other,
see the eps
argument below.
‘corx
’ is similar to ‘cor
’, but the
current row/column vectors are compared to the ones corx
steps ago, instead of the ones in the previous step. See the
corx
argument below, that gives the size of the shift.
- cor.limit
The correlation limit for convergence if the
‘cor
’ method is used.
- eps
Limit for convergence if the ‘eps
’ method is
used.
- corx
The number of iterations to use as a shift, for checking
convergence with the ‘corx
’ method.
- oscillation
Logical scalar, whether to look for oscillating
seeds. Usually there are not too many oscillating seeds, so it is
safe to leave this on FALSE
.
- maxiter
The maximum number of iterations allowed.