raivokolde/seqlm

Sequential lm for methylation data

seqlm's Issues

error install package

I got this error message below when try to install seq in linux machine:　　　
Error in iconv(x[ind], "latin1", "ASCII", sub = "byte") : 　　　　object 'ind' not found 　　　　　　Execution halted 　　　　Error in run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), : 　　　｀System command error
please modify description file with Encoding: UTF-8 (this can fix the problem).
Also please remove those warnings of no visible binding variable when checking package(this is quite important for passing check on CRAN and BioConductor)

Problem in seqlm tool

Hi Raio,
I was looking for seqlm tools, I think this is the tool which was used in your research article "DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns". When I am using command which you provided in README file, I am getting this error-
data(tissue_small)
segments = seqlm(values = tissue_small$values, genome_information = tissue_small$genome_information, annotation = tissue_small$annotation)

Error::
Error in seqlm_segmentation(values = values, genome_information = genome_information, :
could not find function "DataFrame"

Can you please suggest me how I can fix this problem.

Thanks
Nitish

Error information

Hello:

I using seqlm for the TCGA data and found the following error information. (i tested the same code for other cancer types, it all passed, but only one of cancer type stop running with such error). Do you have any idea? Thanks.

load("genome_information.RData")
library(doParallel)
library(seqlm)
registerDoParallel(cores = 6)
segments = seqlm(values = beta, genome_information = genome_information, annotation = pheno)

Finding the best segmentation

|=================================================================| 100%

Calculating coefficients and p-values for all regions

Error in avg_matrix(seqlmresults$data$values, segments$length): Lengths does not sum up to number of rows in mat

warning and error using seqlm

When I load seqlm, a warning message shows up: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ when loading ‘seqlm’. I did some research online about this error. Some people suggest to update all packages so I did. But the problem didn't go away. So maybe there is a conflict between ggplot2 and S4Vectors? Some people suggest to use importFrom() selectively, or continue to declare Imports: in the DESCRIPTION file but use ggplot2::Position, etc., in the R code.

Another error I ran into is "Aesthetics must be either length 1 or the same as the data (1): xmin, xmax, ymin, ymax, group, x, y" when using seqlmreport.