qc_filter: MS/NMR data filtering based on RSD of "qc" data

In wanchanglin/mtExtra: More functions for metabolomics data analysis

MS/NMR data filtering based on RSD of "qc" data

Description

MS/NMR data filtering based on RSD of "qc" data

Usage

qc_filter(
  x,
  y,
  thres_rsd = 20,
  f_mv = TRUE,
  f_mv_qc_sam = FALSE,
  thres_mv = 0.3
)

Arguments

x	a data matrix.
y	a character string with contents of "sample", "qc" and "blank".
thres_rsd	threshold of RSD on QC. Features less than this threshold will be kept.
f_mv	a flag indicating whether or not to performance missing value filtering on either "sample" or "qc" data.
f_mv_qc_sam	a flag for filtering using percentage of missing values on "qc" or "sample". TRUE is for "qc".
thres_mv	threshold of missing values. Features less than this threshold will be kept.

Details

This filter process takes two steps. First, the missing values filtering is performed on either "qc" or "sample". Then RSD-based filtering is applied to "qc" data.

Value

a list of with contents:

• dat the filtered data matrix

• idx a logical vector of index for keeping features.

See Also

Other variable filters: blank_filter(), locfdr_filter(), mv_filter(), rsd_filter(), var_filter()

wanchanglin/mtExtra documentation built on Aug. 2, 2024, 5:47 p.m.