<< Peaks alignment Peaks alignment (X->X) Other pretaitments >>

fact >> Peaks alignment > obiwarp

obiwarp

correction of retention times in liquid and gaz chromatography

Calling sequence

x2_new_rt=obiwarp(x1_master,x2_slave,score,local,nostdnrm,factors,gaps,init_penalty,response)

Arguments

x1_master:

a Div structure or a matrix of dimensions (n1 x q)

x2_slave:

a Div structure or a matrix of dimensions (n2 x q)

score:

the score function; 4 possibilities:

'cor': Pearson correlation coefficient (by default)

'cov' : covariance

'prd' : dot product

'euc' : Euclidian distance

local:

local alignement rather than global (by default)

nostdnrm:

no standard normalization; by default the score matrix values are mean centered and divided by the standard deviation (unless all values are equal)

factors:

local weighting applied to diagonal/gap moves in alignment; two numbers between entre brackets separated by a comma

ex: [2,1] gives an unbiased alignment

gaps:

gap penalties, initiate then extend; two numbers between brackets separated by a comma

the default values are:

'cor'-> [0.3, 2.4]

'cov' -> [0,11.7]

'prd' -> [0,7.8]

'euc' -> [0.9,1.8]

init_penalty:

penalty for initiating alignment (for local alignment only)

by default: 0

response:

responsiveness of warping; 0 will give a linear warp based on start and end points; 100 will use all bijective anchors

x2_new_rt:

a vector of dimensions (n2 x 1)

Examples

x2_new_rt=obiwarp(x1,x2,'cov',[],[],[2.1,1],[0,11.7],0,30);

Bibliography

Authors


Report an issue
<< Peaks alignment Peaks alignment (X->X) Other pretaitments >>