abagen.io.read_tpm¶

abagen.io.read_tpm(fname, copy=False)[source]¶

Loads RNAseqTPM.csv file found at fname

RNAseq TPM files contain TPM values for all the tissue samples taken from a single donor across all genes. TPM values are scaled fragment (read) counts derived using RSEM.

Parameters

fname (str) – Path to RNAseqTPM.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 TPM 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