5.2 Custom seed matrices
By default, normpatch uses the bundled arab dataset,
an Arabidopsis thaliana RNA-seq count matrix,
to construct the population of mean and variance parameters used for simulation.
## mock1 mock2 mock3 hrcc1 hrcc2 hrcc3
## AT1G01010 35 77 40 46 64 60
## AT1G01020 43 45 32 43 39 49
## AT1G01030 16 24 26 27 35 20
## AT1G01040 72 43 64 66 25 90
## AT1G01050 49 78 90 67 45 60
## AT1G01060 0 15 2 0 21 8The sim_gene_counts() function can also use a user-supplied count matrix
as the seed population for simulation.
The example below uses the Arabidopsis count matrix stored in docs/data/ath.E-MTAB-4391.txt
as the seed matrix.
seed_counts <- read.table("data/ath.E-MTAB-4391.txt", header = TRUE, sep = "\t", row.names = 1)
seed_counts <- as.matrix(seed_counts)
seed_counts <- rbind(seed_counts[, 1:3], seed_counts[, 4:6])
seed_counts <- seed_counts[rowSums(seed_counts) > 0, , drop = FALSE]
head(seed_counts)## control_1 control_2 control_3
## AT1G01010 558 457 392
## AT1G01020 442 345 274
## AT1G01030 33 27 21
## AT1G01040 1149 843 703
## AT1G01046 12 12 19
## AT1G01050 2013 1744 1585The simulated count matrix can then be generated from this seed.
set.seed(1)
x <- sim_gene_counts(seed_counts = seed_counts, fc_mean = c(2, 2))
is_DEG <- def_DEG(x, fc = 2)
x <- calc_nf(x)
gene_colors <- ifelse(is_DEG, "#B24745", "#ADADAD")
plot_ma(x, col = gene_colors)