Hi qiimers! I am using method sparcc and I'd like to know which is the p value and boostrap setting by default to calculate the correlations.

I have been looking for about some information but I have not found anything.

Thanks in advance

Deb!

Hi qiimers! I am using method sparcc and I'd like to know which is the p value and boostrap setting by default to calculate the correlations.

I have been looking for about some information but I have not found anything.

Thanks in advance

Deb!

Hello Deb!

Can you post the full command you ran? I can see if I can find it in the source of the plugin.

2 Likes

Hi Colin! These are the commands tan I usually run.

(qiime2-2021.2) [email protected]:~/$ qiime SCNIC sparcc-filter --i-table table_C_order.qza --o-table-filtered table_C_order_nofilt_scnic.qza

Saved FeatureTable[Frequency] to: table_C_order_nofilt_scnic.qza

(qiime2-2021.2) [email protected]:~/$ qiime SCNIC calculate-correlations --i-table table_C_order_nofilt_scnic.qza --p-method sparcc --o-correlation-table table_C_order_nofilt_correls.qza

Saved PairwiseFeatureData to: table_C_order_nofilt_correls.qza

(qiime2-2021.2) [email protected]:~/$ qiime SCNIC build-correlation-network-r --i-correlation-table table_C_order_nofilt_correls.qza --p-min-val 0.50 --o-correlation-network table_C_order_nofilt_sparcc_net.qza

Saved Network to: table_C_order_nofilt_sparcc_net.qza

(qiime2-2021.2) [email protected]:~$ qiime tolos export --input-path table_C_order_nofilt_sparcc_net.qza --output-path Biom_C_order_nofilt_sparcc/

Exported table_C_order_nofilt_sparcc_net.qza as GraphModelingLanguageDirectoryFormat to directory Biom_C_order_nofilt_sparcc/

For the first filter command,

For bootstrap and p-value:

So 1000 bootstrap iterations

False discovery rate correction with Benjamini Hochberg (not that you asked, but there it is!)

So p < 0.05 by default

Digging into the code can be pretty messy. I hope this helped.

If anyone can find docs on these, that would be even better!