Description Usage Format Source References Examples
KEGG pathway abundance data from PICRUSt analysis. This is monthly longitudinal data of 50 infants from birth to 2 years of life.
1 |
A list of 2 dataframes for level 1 and level 2 of KEGG pathways.
Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421. (PubMed)
1 2 3 4 5 6 7 8 9 10 11 | data(kegg.12)
# Load covariate data
data(covar.rm)
# Comparison of pathway relative abundances for some first pathways of level 1 only
# and assuming crosssectional data (to save running time)
path1<-pathway.compare(pathtab=list(kegg.12[[1]][, 1:2]),
mapfile=covar.rm,sampleid="sampleid",pathsum="rel", stat.med="gamlss",
comvar="gender",adjustvar=c("age.sample","bf"), longitudinal="no",
p.adjust.method="fdr", percent.filter=0.05,relabund.filter=0.00005)
taxcomtab.show(taxcomtab=path1$l1, sumvar="path",tax.lev="l2",
tax.select="none", showvar="genderMale", p.adjust.method="fdr",p.cutoff=1)
|
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: ‘gamlss.data’
The following object is masked from ‘package:datasets’:
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.2-0 **********
For more on GAMLSS look at https://www.gamlss.com/
Type gamlssNews() to see new features/changes/bug fixes.
[1] 1
******************************************************************
Family: c("BEZI", "Zero Inflated Beta")
Call: gamlss::gamlss(formula = stats::as.formula(paste(pathname[i],
paste(c(comvar, adjustvar), collapse = "+"), sep = "~")),
family = BEZI, data = testdat, trace = FALSE)
Fitting method: RS()
------------------------------------------------------------------
Mu link function: logit
Mu Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -2.246380 0.019984 -112.410 < 2e-16 ***
genderMale 0.004272 0.014308 0.299 0.765
age.sample 0.008404 0.001235 6.804 1.76e-11 ***
bfNon_exclusiveBF -0.022727 0.023196 -0.980 0.327
bfNo_BF 0.042615 0.038138 1.117 0.264
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
------------------------------------------------------------------
Sigma link function: log
Sigma Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.36087 0.04449 120.5 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
------------------------------------------------------------------
Nu link function: logit
Nu Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -21.43 866.54 -0.025 0.98
------------------------------------------------------------------
No. of observations in the fit: 995
Degrees of Freedom for the fit: 7
Residual Deg. of Freedom: 988
at cycle: 7
Global Deviance: -4914.618
AIC: -4900.618
SBC: -4866.299
******************************************************************
******************************************************************
Family: c("BEZI", "Zero Inflated Beta")
Call: gamlss::gamlss(formula = stats::as.formula(paste(pathname[i],
paste(c(comvar, adjustvar), collapse = "+"), sep = "~")),
family = BEZI, data = testdat, trace = FALSE)
Fitting method: RS()
------------------------------------------------------------------
Mu link function: logit
Mu Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.246380 0.019984 112.410 < 2e-16 ***
genderMale -0.004272 0.014308 -0.299 0.765
age.sample -0.008404 0.001235 -6.804 1.76e-11 ***
bfNon_exclusiveBF 0.022727 0.023196 0.980 0.327
bfNo_BF -0.042615 0.038138 -1.117 0.264
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
------------------------------------------------------------------
Sigma link function: log
Sigma Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.36087 0.04449 120.5 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
------------------------------------------------------------------
Nu link function: logit
Nu Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -21.43 866.54 -0.025 0.98
------------------------------------------------------------------
No. of observations in the fit: 995
Degrees of Freedom for the fit: 7
Residual Deg. of Freedom: 988
at cycle: 7
Global Deviance: -4914.618
AIC: -4900.618
SBC: -4866.299
******************************************************************
Warning messages:
1: In summary.gamlss(gamlss::gamlss(stats::as.formula(paste(pathname[i], :
summary: vcov has failed, option qr is used instead
2: In summary.gamlss(gamlss::gamlss(stats::as.formula(paste(pathname[i], :
summary: vcov has failed, option qr is used instead
id Estimate.genderMale ll ul
1 Cellular.Processes 0 -0.02 0.03
2 Environmental.Information.Processing 0 -0.03 0.02
Pr(>|t|).genderMale pval.adjust.genderMale
1 0.7654 0.7654
2 0.7654 0.7654
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