The default value of 'abundanceCol'
1
0
Entering edit mode
Jinghua • 0
@5072e19c
Last seen 20 days ago
Hong Kong

Hi! I'm using tximport to summarize transcript-level abundance to get gene-level abundance. I didn't specify a value to 'abundanceCol', and I got an abundance matrix in the result. I wonder what's the default value of 'abundanceCol'. Thanks!

tximportData • 162 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 3 days ago
United States

The default is dependent on the input. Mostly it's TPM, but for e.g., StringTie it's FPKM. You can always see the function body by typing the function name at the command prompt.

0
Entering edit mode

Hi, James. I'm using kallisto. I checked the function body and indeed the default value is TPM. Thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 566 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6