DESCRIPTION
, rain
to v0.5.1
.dmapaq
to v0.3.4
.NACHO
.rain
.DESCRIPTION
, dgapaq
to v0.6.0
.DESCRIPTION
, dgapaq
to v0.5.2
.dmapaq
to v0.3.3
.DESCRIPTION
, dmapaq
to v0.3.2
DESCRIPTION
, dgapaq
to v0.5.1
.dmapaq
to v0.3.1
.rain
to v0.5.0
.DESCRIPTION
, Imports
.dgapaq
to v0.2.0
.dmapaq
to v0.2.0
.rain
to v0.4.0
.dgapaq
:R/qc_impute.R
.R/qc_plinky.R
.inst/perl/HRC-1000G-check.bim.pl
.dmapaq
:R/qc_idats.R
.R/read_idats.R
.R/ggheatmap.R
.umr1283
from the list of attached packages.R/utils-pipe.R
.R/utils-tidy-eval.R
.umr1283
.MiSTr
.rain
.NACHO
.forcats
.stringr
.dplyr
.purrr
.readr
.tidyr
.tibble
.ggplot2
.R/mist.R
, now attaches the R package MiSTr
.R/estimate_ethnicity.R
, now attaches the R package rain
.qc_idats
from umr1283
.qc_impute
from umr1283
.qc_plink
from umr1283
.R/qc_idats.R
, mist()
, it allows to test for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statisticsR/pca_report.R
, inst/rmarkdown/qc_idats.Rmd
, R/qc_idats.R
, R/estimate_ethnicity.R
, inst/rmarkdown/qc_idats.Rmd
, as.data.frame
.R/estimate_ethnicity.R
, complete roxygen documentation.inst/rmarkdown/qc_plink.Rmd
,file-management
chunk, each plink steps to prepare files for imputation now
generate different files to avoid names conflicts.R/qc_idats.R
,"MethPipe"
with "CARoT"
in messages.inst/rmarkdown/qc_idats.Rmd
,qc_impute()
, it allows to compute post-imputation quality-control report using a default rmarkdown template (inst/rmarkdown/qc_impute.Rmd
).inst/rmarkdown/qc_plink.Rmd
,R/estimate_ethnicity.R
, if
statement when testing the parameters:
input_type = "array"
and splitted_by_chr = FALSE
.bin_path
argument.check_*
functions.compute_pca()
.vcf_half_call
parameter to handle half-call when converting VCF to PLINK format.R/qc_plink.R
,n_cores
to make it consistent with the current default values.cohort_name
parameter.R/qc_idats.R
,cohort_name
.n_cores
to make it consistent with the current default values.inst/rmarkdown/qc_plink.Rmd
,R/pca_report.R
, fix merge issue when the selected column was not "Sample_ID"
(@mboissel, #2).inst/rmarkdown/qc_plink.Rmd
,include = FALSE
for chunk without figure, table or text output. na.rm = TRUE
in geom_point()
calls.tidyr::separate()
in relatedness_03
chunk by setting a more complex separator, i.e., "_-_"
.exclusion
chunk.R/qc_plink.R
,inst/rmarkdown/qc_plink.Rmd
.R/qc_idats.R
,R/pca_report.R
, R/estimate_ethnicity.R
, qc_plink()
, it allows to compute quality-control of genotyping array (PLINK format) using a default rmarkdown template (inst/rmarkdown/qc_plink.Rmd
).DESCRIPTION
, add RSpectra (<= 0.13-1) for flashpcaR to Imports
.DESCRIPTION
, add data.table and qdap to Imports
.inst/rmarkdown/qc_idats.Rmd
, parameters are now described using question "should ... be removed?"
instead of "remove ...".inst/rmarkdown/qc_idats.Rmd
, now includes a section with the parameters used.R/qc_idats.R
, fix a typo in the detection_pvalues
parameter's documentation.R/estimate_ethnicity.R
, add roxygen2 documentation for estimate_ethnicity()
.R/ggheatmap.R
, add roxygen2 documentation for ggheatmap()
.R/pca_report.R
, add roxygen2 documentation for pca_report()
.R/qc_idats.R
, add roxygen2 documentation for qc_idats()
.man
, add roxygen2 documentation for estimate_ethnicity()
, ggheatmap()
, pca_report()
and qc_idats()
.inst/rmarkdown/qc_idats.Rmd
, fix markdown typos.inst/rmarkdown/qc_idats.Rmd
, fix Methods section describing what filter_
parameters do.R/qc_idats.R
, decrease default dpi value from 300
to 120
.inst/rmarkdown/qc_idats.Rmd
, fix the bullet list in gender check section.R/estimate_ethnicity.R
, add check_input()
function to properly check inputs using fs
package.inst/rmarkdown/qc_idats.Rmd
, now print call rate parameters in plain text.inst/rmarkdown/qc_idats.Rmd
and R/qc_idats.R
, qc_idats()
has a new cache
parameter.format_sequencing()
(R/estimate_ethnicity.R
), fix missing arguments from format_vcf()
.inst/rmarkdown/qc_idats.Rmd
, now applies filter_xy
after gender check.inst/rmarkdown/qc_idats.Rmd
, fix Sample_ID
(i.e., rownames) for gender check.R/qc_idats.R
, remove cat()
messages from ENmix
functions.read_idats()
, it allows to efficiently import idats files mostly using minfi
functions.estimate_ethnicity()
, it allows to compute the genomic component for ethnicity based on VCF files.pca_report()
, it allows to compute an analysis report using principal component analysis.
The function can be used in Rmarkdown chunk with results="asis"
to render the report.ggheatmap()
, it allows to compute heatmap with dendrogram on x-axis and y-axis.qc_idats()
, it allows to compute quality-control of methylation array from Illumina using a default rmarkdown template (inst/rmarkdown/qc_idats.Rmd
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