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davismcc / archive-scater

An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
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exprs documentation #101

Closed rspreafico closed 7 years ago

rspreafico commented 7 years ago

In any function with an exprs_values argument, both tpm and exprs are indicated as being used by default (scater 1.3.42):

exprs_values
character string indicating which values should be used as the expression values for this plot. Valid arguments are "tpm" (default; transcripts per million), "norm_tpm" (normalised TPM values), "fpkm" (FPKM values), "norm_fpkm" (normalised FPKM values), "counts" (counts for each feature), "norm_counts", "cpm" (counts-per-million), "norm_cpm" (normalised counts-per-million), "exprs" (whatever is in the 'exprs' slot of the SCESet object; default), "norm_exprs" (normalised expression values) or "stand_exprs" (standardised expression values) or any other slots that have been added to the "assayData" slot by the user.

davismcc commented 7 years ago

Thanks for the report! I have cleaned these up (usual default is "exprs", though this can vary depending on the function, e.g. plotHighestExprs). Fixed docs will appear in the next push.

Best wishes Davis