Arguments
maxChromThreshold
Chromosomes are ordered and numbered as
usual, except for X and Y chromosome, which in for Homo sapiens
genome have numbers 23 and 24 respectively, in for Mus musculus 20
and 21, etc. Remove chromosomes from segmentation analysis which are
greater than this value.
minChromThreshold
Chromosomes are ordered and numbered as
usual, except for X and Y chromosome, which in for Homo sapiens
genome have numbers 23 and 24 respectively, in for Mus musculus 20
and 21, etc. Remove chromosomes from segmentation analysis which are
lower than this value.
method.of.averaging
If left as the default no combining of replicate
spots takes place. Otherwise this should specify a function which takes a
vector of duplicates and combines them into a single value.
ID
Name of column in RG\$genes corresponding to the clone names.
For most data the default will work, however for affy data the value for ID
should be "CloneName"
prop.missing
For each probe the proportion of NA's is
calculated, and the probe is kept for further analysis if the
proportion of NA's is less than missing.prop