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Prepare SomaScan protein data

prepare_somascan_data.Rd

This functions prepares a data set of SomaScan protein data given the raw CKB SomaScan data.

Usage

prepare_somascan_data(
  data,
  sample_data,
  meta_data,
  transform = c("log2", "log", "log10", "none"),
  qc = c("default", "flagged", "none"),
  repeat_samples = c("remove", "retain"),
  columns = NULL
)

Arguments

data

Raw CKB SomaScan protein data (imported from data_baseline_somalogic.rds or data_baseline_somalogic.csv)

sample_data

Raw CKB SomaScan protein sample information data (imported from data_baseline_somalogic_samples.rds or data_baseline_somalogic_samples.csv)

meta_data

SomaScan meta data produced by prepare_somascan_meta_data().

transform

Transformation to apply to protein values:

  • "log2" (default): log base 2

  • "log10": log base 10

  • "none"

qc

QC steps to apply.

  • "default" (default): Exclude participant samples with hybridization control scale factor out of range.

  • "flagged": Exclude participants samples flagged for any normalization acceptance criteria.

  • "none": Do not exclude any participant samples.

repeat_samples

Default "remove" will remove data for the second sample for participants who had a sample run twice. Use "retain" to keep this data; the second samples will have sample_source=1.

columns

Names of any additional columns from sample_data to include in the output.

QC acceptance criteria

Hybridization control scale factor (hybcontrolnormscale) and median signal normalization scale factors (normscale_20, normscale_0_5, normscale_0_005) have an acceptance range of 0.4-2.5.

Percentage of measurements used for ANML scale factor calculation (anmlfractionused_20, anmlfractionused_0_5, anmlfractionused_0_005) has a criteria of > 30% (0.3).

Samples that meet these criteria are given a PASS for normalization acceptance criteria for all row scale factors (rowcheck), while samples that are outside the criteria are given a FLAG.

Hybridization control scale factor out of range suggests a technical issue. Set qc = "default" to exclude participant samples with hybridization control scale factor (hybcontrolnormscale) out of range (i.e. less than 0.4 or greater than 2.5).

Other criteria out of range suggests that the sample is fairly different from a typical population. Set qc = "flagged" to exclude participant samples with a FLAG for normalization acceptance criteria for all row scale factors (rowcheck).