ATAC-seq chromatin accessibility data from 123 acute myelogenous leukemia (AML) patient samples and 5 healthy hematopoietic stem/progenitor cell (HSPC) samples. The dataset contains chromatin accessibility measurements across 824 genomic regions.
Format
A matrix (dense) with 824 rows (genomic regions) and
135 columns (samples). Sample metadata is stored as an attribute.
The data is stored as dense because it has very low sparsity (~0.2% zeros).
Access metadata via attr(aml, "metadata_h"), which contains:
- samples
Character vector of sample IDs
- category
Character vector indicating sample type (AML subtype or HSPC)
Source
Corces et al. (2016). "Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution." Nature Genetics 48(10): 1193-1203.
Details
This dataset contains ATAC-seq chromatin accessibility data for studying acute myelogenous leukemia. Samples represent different AML subtypes including:
Common myeloid progenitors (CMP)
Granulocyte-monocyte progenitors (GMP)
Lymphoid-primed multi-potent progenitors (LMPP)
Megakaryocyte-erythrocyte progenitors (MEP)
Multi-potent progenitors (MPP)
Healthy hematopoietic stem/progenitor cells (HSPC)
Examples
# \donttest{
# Load dataset
data(aml)
# Inspect structure
dim(aml)
#> [1] 824 135
table(attr(aml, "metadata_h")$category)
#>
#> AML (GMP) AML (L-MPP) AML (MEP) Control (GMP) Control (L-MPP)
#> 93 12 15 5 5
#> Control (MEP)
#> 5
# Run NMF (transpose so samples are columns)
result <- nmf(t(aml), k = 6, maxit = 100)
# }