abagen.io.read_counts

abagen.io.read_counts(fname, copy=False)

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:

• fname (str) – Path to RNAseqCounts.csv file

• copy (bool, optional) – Whether to return a copy if fname is a pre-loaded pandas.Dataframe. Default: False

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 with read_annotation().

Return type:

(G, S) pandas.DataFrame