norm.data {iCellR} | R Documentation |
This function takes an object of class iCellR and normalized the data based on "global.glsf", "ranked.glsf" or "spike.in" methods.
norm.data( x = NULL, norm.method = "ranked.glsf", top.rank = 500, spike.in.factors = NULL, rpm.factor = 1000 )
x |
An object of class iCellR. |
norm.method |
Choose a normalization method, there are three option currently. Choose from "global.glsf", "ranked.glsf","spike.in" or no.norm, default = "ranked.glsf". |
top.rank |
If the method is set to "ranked.glsf", you need to set top number of genes sorted based on global base mean, default = 500. |
spike.in.factors |
A numeric vector of spike-in values with the same cell id order as the main data. |
rpm.factor |
If the norm.method is set to "rpm" the library sizes would be divided by this number, default = 1000 (higher numbers recomanded for bulk RNA-Seq). |
An object of class iCellR.
demo.obj <- norm.data(demo.obj, norm.method = "ranked.glsf", top.rank = 500)