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✍️ Update data types description
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raevskymichail committed Feb 1, 2023
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Showing 1 changed file with 12 additions and 17 deletions.
29 changes: 12 additions & 17 deletions README.md
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Expand Up @@ -43,7 +43,7 @@ install_github("raevskymichail/epi-impute/epi.impute")
Download source codes and then type in R session:

```r
install.packages(path_to_archive, type = 'source', rep = NULL)
install.packages(path_to_archive, type = "source", rep = NULL)
```

Where `path_to_archive` would represent the full path and file name:
Expand All @@ -63,25 +63,20 @@ data_imputed <- epi_impute(sc_exp_data = data[["sc_exp_data"]],
sc_atac_peaks_ann = data[["sc_atac_peaks_ann"]],
cell_types = c("HSC", "CMP", "GMP"))
```

Where

**sc_exp_data** a single-cell RNA-seq count matrix, where rownames are
HGNC genes (HUGO) and colnames are cell ids
**sc_atac_data** a single-cell ATAC-seq count matrix, where rownames are
cell ids and colnames are ids for euchromatine peaks (obtained from peak caller,
for ex. MACS2)
**sc_atac_cell_names** a matrix, containing description and annotation for
cell types observed in scATAC-seq count matrix. It should have rownames (cell
ids) that
match rownames of `sc_atac_data`
**sc_atac_peaks_ann** a matrix, containing description for euchromatine
peaks, presented in count matrix. It should have rownames (peak ids) that
match colnames of `sc_atac_data`
**cell_types** a vector, containing names for cell types, presented in
count matrix.
**atac_bin_thrld** a numeric value for accessibility threshold used for
primary binirization of peaks in scATAC-seq matrix.
**sc_exp_data** – scRNA-seq count matrix, where rownames are HGNC genes (HUGO) and colnames are *cell ids*

**sc_atac_data** – scATAC-seq count matrix, where rownames are *cell ids* and colnames are ids for euchromatine peaks (obtained from peak caller, for ex. MACS2)

**sc_atac_cell_names** – matrix, containing description and annotation for cell types observed in scATAC-seq count matrix. It should have rownames (*cell ids*) that match rownames of `sc_atac_data`

**sc_atac_peaks_ann** – matrix with annotations (coordinates) for euchromatine peaks, presented in the scATAC-seq count matrix. It should have rownames (*peak ids*) that match colnames of `sc_atac_data`

**cell_types** – vector, containing names for cell types, presented in count matrix.

**atac_bin_thrld** – numeric value for accessibility threshold used for primary binirization of peaks in scATAC-seq matrix.

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