Usage
msap(datafile, name=datafile, no.bands = "u", nDec=4, meth=TRUE, rm.redundant=TRUE, rm.monomorphic=TRUE, do.pcoa=TRUE, do.shannon=TRUE, do.amova=TRUE, do.pairwisePhiST=FALSE, do.cluster=TRUE, use.groups=NULL, do.mantel=FALSE, np.mantel=1000, loci.per.primer=NULL, error.rate.primer=NULL, uninformative=TRUE)
Arguments
datafile
String containing the url of the csv file with the data. Required.
name
a name for the dataset to be included in the output files. By default, the name of the given datafile is used.
no.bands
String to indicate how to deal with HPA-/MSP- pattern in MSL, with two possible values: 'h' for hypermethylated state and 'u' for uninformative state (default).
With 'h' researcher assumes that HPA-/MSP- (no band for both isoschizomers) pattern represents full methylation of cytosines in the target (hypermethylation) ignoring the chance of genetic change in the target. This approach could be very useful when no much genetic differences are expected between samples (i.e. the same individuals are compared for different treatments). In this case HPA-/MSP- will compute as 'methylated' state in the binary matrix used for subsequent analysis.
With 'u' (default value), researcher considers that pattern as uninformative as could be caused by a missing target (mutation) as well as by hypermethylation. So, in this case, HPA-/MSP- will compute as missing values in the binary matrix used for subsequent analysis.
nDec
number of digits of precision for floating point output.
meth
Logical value switching between MSAP ('TRUE') and standard AFLP ('FALSE') analysis. The difference lies in that for AFLP (meth=FALSE) the 'enzyme' column is ignored and every row in data represent an independent sample, without combination of data.
rm.redundant
Not implemented yet.
rm.monomorphic
Logical value switching between the removal ('TRUE', by default) of monomorphic fragments (defined as those with only one state or just one ocurrence of the second state across the whole dataset) after data transformation.
do.pcoa
Option switcher for doing a Principal Coordinate Analysis for variation between groups. TRUE by default.
do.shannon
Option switcher for Shannon's Diversity Index comparison between MSL and NML.
do.amova
Option switcher for doing an AMOVA for differentiation between groups. TRUE by default.
do.pairwisePhiST
Logical value switching between the calculation of the pairwise Phi_st between pairs of groups/populations ('TRUE' ) or skip it ('FALSE' by default).
do.cluster
Calculates and plots a Neighbour-Joining tree ('TRUE' by default) or skip it ('FALSE').
use.groups
Gives the groups/populations/treatments of the datafile to be analysed. By default all groups are considered into de the analysis. To provide a subset of the groups a vector should be passed with the names of groups to be included. For example, in a datafile with 5 groups (Control, pop1, pop2, pop3 and pop4) we are interested only in Control and pops 1 and 3. Then, msap should be called with 'use.groups=c('Control','pop1','pop3')'.
do.mantel
Performs a Mantel test to obtain correlation between MSL and NML ('TRUE') or skip it ('FALSE' by default).
np.mantel
Gives the number of permutations for the above Mantel test (1000 by default) or skip it ('FALSE').
loci.per.primer
Vector providing the number of loci/fragements obtained per primer combination. Fragment classsification is performed independenty for each primer combination. These fragment should be ordered in the datafilein the sameway as specified here. If this is nor provided (by default) then all fragments should be analyzed as they come from a single combination. For example, if there are three primer combinations with 135, 234 and 210 loci each, then msap should be called with 'loci.per.primer=c(135,234,210)'
error.rate.primer
Gives the repeatibility value of MSAP assays for each primer combination. It provides a threshold to consider methylation events as genotyping errors.
uninformative
Deprecated. This argument is keept for back compatibility with version 1.0.x. Contains the same information as no.bands.