Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds

[ChengHsiangLu]

Hi,

I've created my 1-column count matrix with featureCounts. However, after creating my count_mat and df_allele, it still shows an error when I try run_numbat.

The code I use is as follows:

library(numbat)
library(Matrix)
library(dplyr)

## count_mat by featureCounts
CPM00000383_count_mat <- as.matrix((read.table("/Users/samuellu/Desktop/Labs/CHLA_Lab/Numbat/CPM00000383-BM-R_20210510/count_mat.csv", sep = ",")))
colnames(CPM00000383_count_mat) <- c('CPM00000383-BM-R_20210510')
CPM00000383_count_mat_dgC <- as(CPM00000383_count_mat, "dgCMatrix") 

## df_allele
CPM00000383_df_allele <- as.data.frame(read.table("/Users/samuellu/Desktop/Labs/CHLA_Lab/Numbat/CPM00000383-BM-R_20210510/CPM00000383-BM-R_20210510_allele_counts.tsv", sep = "\t", header = T))


bulk <- get_bulk(
  count_mat = CPM00000383_count_mat_dgC,
  lambdas_ref = ref_hca,
  df_allele = CPM00000383_df_allele,
  gtf = gtf_hg38)

segs_loh <- bulk %>% detect_clonal_loh(t = 1e-4)


out <- run_numbat(
  CPM00000383_count_mat_dgC, 
  ref_hca, 
  CPM00000383_df_allele, 
  ncores = 4,
  plot = TRUE,
  out_dir = './test/CPM00000383',
  segs_loh = segs_loh
)

This is the error message I got after run_numbat.

Running under parameters:
t = 1e-05
alpha = 1e-04
gamma = 20
min_cells = 50
init_k = 3
max_cost = 0.3
max_iter = 2
max_nni = 100
min_depth = 0
use_loh = auto
multi_allelic = TRUE
min_LLR = 5
min_overlap = 0.45
max_entropy = 0.5
skip_nj = FALSE
diploid_chroms = 
ncores = 4
ncores_nni = 4
common_diploid = TRUE
tau = 0.3
check_convergence = FALSE
plot = TRUE
genome = hg38
Input metrics:
1 cells
Mem used: 0.414Gb
Approximating initial clusters using smoothed expression ..
Mem used: 0.414Gb
number of genes left: 9313
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds

Can you share with me where is the problem that causes this error?

Thanks,
Sam

[teng-gao]

Closing this issue as I answered it in the original thread (#53 ).