Closed lcolladotor closed 6 years ago
Here are the numbers. Note that for BrainSeq we are using Dx == 'Control'
only.
library('SummarizedExperiment')
type <- 'gene'
load_file <- file.path(
'/dcl01/lieber/ajaffe/lab/brainseq_phase2/expr_cutoff',
paste0('rse_', type, '.Rdata'))
load(load_file)
colData(rse_gene)$age_group <- ifelse(colData(rse_gene)$Age >= 18, 'adult', ifelse(colData(rse_gene)$Age <= 0, 'fetal', 'other'))
colData(rse_gene)$Region <- relevel(factor(colData(rse_gene)$Region), 'DLPFC')
with(colData(rse_gene), addmargins(table(age_group, Region, Dx)))
load_file <- file.path(
'/dcl01/lieber/ajaffe/lab/brainseq_phase2/brainspan',
paste0('rse_span_', type, '.Rdata'))
load(load_file)
colData(rse_span_gene)$age_group <- ifelse(colData(rse_span_gene)$Age >= 18, 'adult', ifelse(colData(rse_span_gene)$Age <= 0, 'fetal', 'other'))
with(colData(rse_span_gene), addmargins(table(age_group, Region)))
## BrainSeq
, , Dx = Control
Region
age_group DLPFC HIPPO Sum
adult 222 238 460
fetal 29 28 57
other 49 48 97
Sum 300 314 614
, , Dx = Schizo
Region
age_group DLPFC HIPPO Sum
adult 152 132 284
fetal 0 0 0
other 1 1 2
Sum 153 133 286
, , Dx = Sum
Region
age_group DLPFC HIPPO Sum
adult 374 370 744
fetal 29 28 57
other 50 49 99
Sum 453 447 900
## BrainSpan
Region
age_group DLPFC HIPPO Sum
adult 8 8 16
fetal 18 18 36
other 14 13 27
Sum 40 39 79
For the number of individuals used in the regional difference analysis.
> span_reg <- rse_span_gene[, colData(rse_span_gene)$age_group %in% c('adult', 'fetal')]
> dim(span_reg)
[1] 24652 52
> length(colData(span_reg)$Braincode)
[1] 52
> length(unique(colData(span_reg)$Braincode))
[1] 26
Overall numbers used for the development analysis:
> dim(rse_span_gene)
[1] 24652 79
> length(unique(colData(rse_span_gene)$Braincode))
[1] 41
> length(colData(rse_span_gene)$Braincode)
[1] 79
Both for BrainSeq and BrainSpan