abagen.io.read_counts¶
- abagen.io.read_counts(fname, copy=False)[source]¶
Loads RNAseqCounts.csv file found at fname
RNAseq count files contain fragment counts for all the tissue samples taken from a single donor across all genes. Fragment counts can be fractional, as ambiguous reads are distributed between relevant transcripts. For present / absent calling, a value of zero indicates no transcript was seen.
- Parameters
- Returns
tpm – Dataframe containing RNAseq count expression data, where G is genes and S is samples. The row index is the unique gene symbol assigned during processing, which can be used to match data to the information obtained with
read_genes()
. The column index is the unique sample ID (integer, beginning at 0) which can be used to match data to the information obtained withread_annotation()
.- Return type
(G, S) pandas.DataFrame