r - convert table type from character/list to numeric (maSigPro, time series analysis, p.vector) -


i totally new r , perfom time series analysis masigpro package, based on different count tables.

at moment struggling data type p.vector function. table tpm normalized counts read in follows:

counts_tpm =  as.matrix(read.table("tpm_counts_25min.txt",  header=t,      row.names=1, stringsasfactors=false) counts_tpm=as.data.frame(counts_tpm, stringsasfactors=false)  typeof(counts_tpm) # [1] "list"

this data type doesn't fit p.vector function:

fit=p.vector(counts_tpm, sample_des_design, q=0.05, counts=true) # **error** in fun(newx[, i], ...) : invalid 'type' (character) of argument

this short outtake of tpm normalized count table:

        e15r003a06  e15r003b06   e15r003c06  e15r003d13   e15r003d12           12.554467 12.68203563 1.436166e+01 13.58263382 1.312083e+01      b    10.392282 14.65197068 1.141320e+01  8.84738000 8.826718e+00      r    39.127930 42.10897757 4.194345e+01 34.76635026 3.005847e+01      x     6.696018  6.64936858 5.897263e+00  4.98501460 4.652471e+00       s    77.418782 84.95649902 8.017746e+01 82.99038040 7.884357e+01      t    53.565504 56.02217626 5.487839e+01 49.47038414 4.341778e+01

i tried read.csv csv format of table , things data.matrix (but function totally messing values), think missing 1 main point ....

i hope can me!


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