Parameters

• bd5info — object returned by getbdinfo
• snp — 1-based integer index or character SNP ID

Return value

A list with four numeric vectors of length n_samples:

• dosage — DS values in \[0, 2\]; NA = missing
• p0 — Pr(g=0) in \[0, 1\]; NA = missing
• p1 — Pr(g=1) in \[0, 1\]; NA = missing
• p2 — Pr(g=2) in \[0, 1\]; NA = missing

Reading a SNP by index

snp1 <- getbd5snp(bd5info = bd5, snp = 1L)

knitr::kable(
  data.frame(
    SampleID = head(bd5$samples$sid, 10),
    Dosage   = round(head(snp1$dosage, 10), 4),
    P_00     = round(head(snp1$p0,     10), 4),
    P_01     = round(head(snp1$p1,     10), 4),
    P_11     = round(head(snp1$p2,     10), 4)
  ),
  caption = paste("SNP", bd5$snps$snpid[1], "— first 10 subjects")
)

Reading a SNP by ID

snp3 <- getbd5snp(bd5info = bd5, snp = "1:12000:T:C")

knitr::kable(
  data.frame(
    SampleID = head(bd5$samples$sid, 10),
    Dosage   = round(head(snp3$dosage, 10), 4),
    P_00     = round(head(snp3$p0,     10), 4),
    P_01     = round(head(snp3$p1,     10), 4),
    P_11     = round(head(snp3$p2,     10), 4)
  ),
  caption = "SNP 1:12000:T:C — first 10 subjects"
)

Using getbd5snp in a loop

getbd5snp is convenient but allocates a new list and opens the file on every call. For a small number of SNPs this is fine. The following calculates the alternate allele frequency for every SNP.

aaf <- numeric(n_snps)
for (i in seq_len(n_snps)) {
  aaf[i] <- mean(getbd5snp(bd5, i)$dosage, na.rm = TRUE) / 2
}

knitr::kable(
  data.frame(snpid = bd5$snps$snpid, aaf = round(aaf, 4)),
  caption = "Alternate allele frequencies via getbd5snp"
)

Parameters

• bd5info — object returned by getbdinfo
• snp — 1-based integer index or character SNP ID
• dosage, p0, p1, p2 — pre-allocated numeric(n_samples) vectors

Return value

NULL invisibly. The four output vectors are updated in place.

Important: R copy-on-modify semantics

The output vectors must not have more than one R binding at the call site. If another variable also points to the same vector, R’s copy-on-modify rule will copy the vector before writing, so the caller’s variable will not be updated. Always use plain, freshly allocated vectors:

# Correct
dosage <- numeric(n_samp)
getbd5snp_buf(bd5, 1L, dosage, p0, p1, p2)

# Wrong — dosage2 creates a second binding; the update may not be visible
dosage2 <- dosage
getbd5snp_buf(bd5, 1L, dosage, p0, p1, p2)

Example

dosage <- numeric(n_samp)
p0     <- numeric(n_samp)
p1     <- numeric(n_samp)
p2     <- numeric(n_samp)

aaf_buf <- numeric(n_snps)
for (i in seq_len(n_snps)) {
  getbd5snp_buf(bd5info = bd5, snp = i, dosage = dosage,
                p0 = p0, p1 = p1, p2 = p2)
  aaf_buf[i] <- mean(dosage, na.rm = TRUE) / 2
}

knitr::kable(
  data.frame(snpid = bd5$snps$snpid, aaf = round(aaf_buf, 4)),
  caption = "Alternate allele frequencies via getbd5snp_buf"
)

Workflow

1. Call openbd5con(bd5info) to open the file and get a "bd5con" object.
2. Call getbd5snp_con inside the loop, passing the "bd5con" object.
3. Call closebd5con when finished to release the file handle promptly. (The connection is also closed automatically when the "bd5con" object is garbage-collected or when R exits, so the explicit close is optional but recommended.)

openbd5con

Opens a persistent connection to the .bdose file.

Parameters

• bd5info — object returned by getbdinfo

Return value

An object of class "bd5con" to be passed to getbd5snp_con and closebd5con.

closebd5con

Explicitly closes the connection.

Parameters

• bd5con — object returned by openbd5con

Return value

NULL invisibly.

getbd5snp_con

Parameters

• bd5info — object returned by getbdinfo
• snp — 1-based integer index or character SNP ID
• dosage, p0, p1, p2 — pre-allocated numeric(n_samples) vectors
• bd5con — object returned by openbd5con

Return value

NULL invisibly. The four output vectors are updated in place.

The same copy-on-modify constraint as getbd5snp_buf applies.

Example

dosage <- numeric(n_samp)
p0     <- numeric(n_samp)
p1     <- numeric(n_samp)
p2     <- numeric(n_samp)

con <- openbd5con(bd5)

aaf_con <- numeric(n_snps)
for (i in seq_len(n_snps)) {
  getbd5snp_con(bd5info = bd5, snp = i, dosage = dosage,
                p0 = p0, p1 = p1, p2 = p2, bd5con = con)
  aaf_con[i] <- mean(dosage, na.rm = TRUE) / 2
}

closebd5con(con)

knitr::kable(
  data.frame(snpid = bd5$snps$snpid, aaf = round(aaf_con, 4)),
  caption = "Alternate allele frequencies via getbd5snp_con"
)